Isolated polypeptides, polynucleotides encoding same, transgenic plants expressing same and methods of using same

ABSTRACT

Nucleic acid constructs are provided. These constructs comprise any of the, nucleic acid sequences at least 85% identical to nucleotide sequences selected from the group consisting of SEQ ID NOs: 68, 1, 4, 5, 8, 9, 11, 13, 16, 19, 20, 23, 24, 27, 30, 32, 37, 42, 49, 50, 51, 53, 54, 55, 56, 57, 58, 64, 69, 70, 73, 77, 78, 79, 80, 84, 86, 87, 93, 94, 98, 101, 102, 103, 104, 105, 106, 107, 108 and 109 and a promoter sequence capable of directing transcription of said nucleic acid sequence in a host cell. Also provided are transgenic plants expressing these nucleic acid constructs and methods of using same.

RELATED APPLICATIONS

This application is a division of U.S. patent application Ser. No. 12/083,978 filed on Apr. 23, 2008, which is a National Phase of PCT Patent Application No. PCT/IL2006/001223 having International filing date of Oct. 24, 2006, which claims the benefit of priority of U.S. Provisional Patent Application No. 60/729,181 filed on Oct. 24, 2005.

U.S. patent application Ser. No. 12/083,978 is also a Continuation-In-Part (CIP) of U.S. patent application Ser. No. 11/629,411 filed on Dec. 13, 2006, now U.S. Pat. No. 7,812,218, which is a National Phase of PCT Patent Application No. PCT/IL2005/000627 having International filing date of Jun. 14, 2005, which claims the benefit of priority of U.S. Provisional Patent Application No. 60/578,833 filed on Jun. 14, 2004.

The contents of the above applications are all incorporated herein by reference.

SEQUENCE LISTING STATEMENT

The ASCII file, entitled 60793SequenceListing.txt, created on Jan. 5, 2015, comprising 2,974,287 bytes, submitted concurrently with the filing of this application is incorporated herein by reference.

FIELD AND BACKGROUND OF THE INVENTION

The present invention relates to isolated polypeptides, polynucleotides encoding same, transgenic plants expressing same and methods of using same. Specifically the present invention can be used to increase fertilizer use efficiency and stress resistance as well as biomass, vigor and yield of transgenic plants.

Fertilizers are the fuel behind the “green revolution”, directly responsible for the exceptional increase in crop yields during the last 40 years. The dramatic rise in crop yields could never have occurred without a parallel increase in fertilizer use. However, in recent years there has been a growing concern with the environmental impact of fertilizer use, particularly nitrogen fertilizers, on water and atmospheric pollution. Limits on fertilizer use have been legislated in several countries, and further restrictions are expected in the future. Greater use of fertilizers will be necessary in the future to support food and fiber production for rapid population growth on limited land resources.

Fertilizer is often mentioned as the number one overhead expense in agriculture. Of the three macronutrients provided as main fertilizers [Nitrogen (N), Phosphate (P) and Potassium (K)], nitrogen is the only one that usually needs to be replenished every year, particularly for cereals, which comprise more than half of the cultivated areas worldwide.

A common approach to promoting plant growth has been, and continues to be, the use of nutrients (fertilizers), natural as well as synthetic. Synthetic nutrients usually provide a macronutrient in a plant-usable form, such as urea for example, and/or inorganic nitrates, phosphates, or the like compounds. While such nutrients may be applied, more or less, at the convenience of the farmer, and may be applied as often as deemed desirable, the overuse of synthetic nutrients and the inefficient use of synthetic nutrients are major factors responsible for environmental problems such as eutrophication of groundwater, nitrate pollution, phosphate pollution, and the like.

Nitrogen is an essential macronutrient for the plant, responsible for biosynthesis of amino and nucleic acids, prosthetic groups, plant hormones, plant chemical defenses, etc. Nitrogen is often the rate-limiting element in plant growth and all field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. Nitrogenous fertilizer, which is usually supplied as ammonium nitrate, potassium nitrate, or urea, typically accounts for 40% of the costs associated with crops such as corn and wheat. It has been estimated that by 2050, more than 150 million tons of nitrogenous fertilizer will used worldwide annually. Increased use efficiency of nitrogen by plants should enable crops to be cultivated with lower fertilizer input, or alternatively on soils of poorer quality and would therefore have significant economic impact in both developed and developing agricultural systems. An overview of the undesirable effects of nitrogen fertilizer is presented by Byrnes, Fertilizer Research, 26, pp. 209-215 (1990). Although plants are able to take up organic nitrogen from the environment, the major part of the nitrogen utilized comes usually from the uptake of inorganic nitrogen in the form of ammonium (NH₄ ⁺) and nitrate (NO₃ ⁻) and its later conversion to organic nitrogen in a process known as assimilation.

The Nitrogen assimilation process begins with NO₃ ⁻ being converted to NH₄ ⁺ sequentially by the enzymes Nitrate Reductase (NR) and Nitrite Reductase (NiR). The nitrogen is then incorporated into Glutamate (Glu) by Glutamine Synthase (GS) to obtain Glutamine (Gln). The major pathway of nitrogen assimilation is the GS/GOGAT cycle (Glutamine Synthase/Glutamate-Oxoglutarate Amine Transferase). The remaining amino acids are synthesized from Gln, Glu and Asn by transamination.

Nitrogen (as amino acids or in the form of nitrates) is translocated to the shoot, where it is stored in the leaves and stalk during the rapid step of plant development and up until flowering. In corn for example, plants accumulate the bulk of their organic nitrogen during the period of grain germination, and until flowering. Once fertilization of the plant has occurred, grains begin to form and become the main sink of plant Nitrogen. The stored Nitrogen can then be redistributed from the leaves and stalk that served as storage compartments until grain formation.

There are three main parameters of efficiency used to define plant Nitrogen metabolism:

Nitrogen-uptake efficiency: is the amount of N in above-ground biomass (gr Nt) divided by the amount of N applied (gr/hectare);

Nitrogen utilization efficiency: is the Grain Yield (gr/plant) divided by the amount of N in above-ground biomass (gr Nt); and

Nitrogen-use efficiency: is the Grain Yield (gr/plant) divided by the amount of N applied (gr/Ha).

The Nitrogen-uptake efficiency [the amount of N in above ground biomass (gr Nt)/N applied (gr/hectare)] is the total amount of nitrogen incorporated by the plant and is a function of the “uptake” (the plant's transport capacity), the metabolic efficiency of the assimilation process and the rate of plant size development, since the mass of stalk and leaves created during growth are the actual Nitrogen-storage organs. The fraction of the assimilated Nitrogen found in a shoot that is ultimately transferred to the grain (yield) is controlled enzymatically, and thus a potential site for transgenic manipulation. This parameter is, in effect, equal to the Nitrogen Utilization efficiency (NUE). Better grain-to-shoot N-partitioning most likely will improve yield and protein content of the grain.

Similarly, the same calculations of use and utilization efficiencies can be made for other macronutrients such as Phosphorous (P) and Potassium (K), which have a direct correlation with yield and general plant tolerance.

The NUE for the main crops ranges from 30-70% only, having a direct negative impact on input expenses for the farmer, due to the excess fertilizer applied, which quickly becomes an ecological burden. Thus, nitrate-containing wastes represent an environmental problem of global significance. Nitrate seepage in water causes eutrophication of lakes, rivers and seas (waters endangered because of algae growth that leads to hypoxia and destruction of marine fauna). Nitrate contamination in drinking water can cause methemoglobinemia, which is especially detrimental to infants and nursing mothers. In fact, the Farming Industry is considered as the largest nitrate polluter of surface and coastal waters and drinking water supplies.

Genetic improvement of Fertilizer Use Efficiency (FUE) in plants can be generated either via traditional breeding or via genetic engineering. However, to date, neither transgenic products nor classically bred enhanced FUE material have been released for commercial use. Among the reasons for this, the most important is that breeders select their elite lines under the most favorable fertilizer conditions, thus overlooking improvements in FUE (yield being the main driver of sales and not reduction in the input costs). Attempts at transgenic solutions for improved FUE are being carried out by companies such as Monsanto (see, for example, US Patent Applications 20020046419 to Choo, et al.; U.S. Pat. Appl. 2005010879 to Edgerton et al.; and U.S. Pat. Appl. 2006 0179511 to Chomet et al), Arcadia Biosciences and Biogemma.

Recently, a review summarizing attempts to improve FUE by transgenic means that have been undertaken by academic laboratories was published (Good A G et al. Trends Plant Sci. 2004 December; 9(12):597-605). Encouraging results were reported by Yanagisawa and coworkers (Proc Natl Acad Sci USA. 2004 May 18; 101(20):7833-8) who found that a genetically engineered increase in carbon skeleton production (2-Oxoglutarate, OG from the GS/GOGAT cycle) sustained growth of transgenic Arabidopsis under low nitrogen conditions. As many enzymes are involved in carbon skeleton production, the transgene was a key transcriptional factor (Dof1) that activated multiple genes involved in the pathway. Nitrogen content was higher in the Arabidopsis transgenic plants by approximately 30% under low nitrogen conditions. U.S. Pat. No. 6,084,153 to Good et al. discloses the use of a stress responsive promoter to control the expression of Alanine Amine Transferase (AlaAT). Good et al. further disclosed that transgenic canola plants improved drought and nitrogen deficiency tolerance when compared to control plants. However, neither the Dof1 constructs of Yanagisawa et al, nor the drought-induced AlaAT constructs of Good et al. have been evaluated in commercial lines, under true field conditions. Hence the economic relevance of the results is yet to be proven.

There is thus a widely recognized need for, and it would be highly advantageous to identify polynucleotides and polypeptides which improve fertilizer use/uptake efficiency in transgenic plants expressing same, which are devoid of the above limitations.

SUMMARY OF THE INVENTION

According to one aspect of the present invention there is provided a nucleic acid construct comprising a nucleic acid sequence at least 85% identical to a nucleotide sequence selected from the group consisting of SEQ ID NOs: 68, 1, 4, 5, 8, 9, 11, 13, 16, 19, 20, 23, 24, 27, 30, 32, 37, 42, 49, 50, 51, 53, 54, 55, 56, 57, 58, 64, 69, 70, 73, 77, 78, 79, 80, 84, 86, 87, 93, 94, 98, 101, 102, 103, 104, 105, 106, 107, 108 and 109 and a promoter sequence capable of directing transcription of the nucleic acid sequence in a host cell.

According to still further features in the described preferred embodiments the nucleic acid sequence is as set forth in SEQ ID NO: 68, 1, 4, 5, 8, 9, 11, 13, 16, 19, 20, 23, 24, 27, 30, 32, 37, 42, 49, 50, 51, 53, 54, 55, 56, 57, 58, 64, 69, 70, 73, 77, 78, 79, 80, 84, 86, 87, 93, 94, 98, 101, 102, 103, 104, 105, 106, 107, 108, 109, 219-767, 1317, 1318, 1319, 1320, 1321, 1322, 1323, 1324, 1325, 1326, 1327, 1328, 1329, 1330, 1331, 1332, 1333, 1334, 1335 or 1336.

According to another aspect of the present invention there is provided an isolated polypeptide, comprising an amino acid sequence at least 85% homologous to the amino acid sequence set forth in SEQ ID NO: 177, 110, 113, 114, 117, 118, 120, 122, 125, 128, 129, 132, 133, 136, 139, 141, 146, 151, 158, 159, 160, 162, 163, 164, 165, 166, 167, 173, 178, 179, 182, 186, 187, 188, 189, 193, 195, 196, 202, 203, 207, 210, 211, 212, 213, 214, 215, 216, 217 or 218.

According to yet another aspect of the present invention there is provided a plant cell comprising an exogenous polynucleotide which comprises a nucleic acid sequence encoding a polypeptide having an amino acid sequence at least 85% homologous to SEQ ID NO: 177, 110, 113, 114, 117, 118, 120, 122, 125, 128, 129, 132, 133, 136, 139, 141, 146, 151, 158, 159, 160, 162, 163, 164, 165, 166, 167, 173, 178, 179, 182, 186, 187, 188, 189, 193, 195, 196, 202, 203, 207, 210, 211, 212, 213, 214, 215, 216, 217 or 218.

According to still further features in the described preferred embodiments the plant cell forms a part of a plant.

According to still further features in the described preferred embodiments the amino acid sequence is as set forth in SEQ ID NO: 177, 110, 113, 114, 117, 118, 120, 122, 125, 128, 129, 132, 133, 136, 139, 141, 146, 151, 158, 159, 160, 162, 163, 164, 165, 166, 167, 173, 178, 179, 182, 186, 187, 188, 189, 193, 195, 196, 202, 203, 207, 210, 211, 212, 213, 214, 215, 216, 217, 218, 768-1051, 1053-1098, 1100-1315 or 1316.

According to still another aspect of the present invention there is provided a method of increasing tolerance of a plant to a stress condition, comprising expressing within the plant an exogenous polynucleotide encoding a polypeptide having an amino acid sequence at least 85% homologous to SEQ ID NO: 177, 110, 113, 114, 117, 118, 120, 122, 125, 128, 129, 132, 133, 136, 139, 141, 146, 151, 158, 159, 160, 162, 163, 164, 165, 166, 167, 173, 178, 179, 182, 186, 187, 188, 189, 193, 195, 196, 202, 203, 207, 210, 211, 212, 213, 214, 215, 216, 217, 218, 1341 or 1343, thereby increasing the tolerance of the plant to the stress condition.

According to an additional aspect of the present invention there is provided a method of increasing biomass, vigor and/or yield of a plant, comprising expressing within the plant an exogenous polynucleotide encoding a polypeptide having an amino acid sequence at least 85% homologous to SEQ ID NO: 177, 110, 113, 114, 117, 118, 120, 122, 125, 128, 129, 132, 133, 136, 139, 141, 146, 151, 158, 159, 160, 162, 163, 164, 165, 166, 167, 173, 178, 179, 182, 186, 187, 188, 189, 193, 195, 196, 202, 203, 207, 210, 211, 212, 213, 214, 215, 216, 217, 218, 1341 or 1343, thereby increasing biomass, vigor and/or yield of the plant.

According to yet an additional aspect of the present invention there is provided a method of increasing fertilizer use efficiency and/or uptake of a plant comprising expressing within the plant an exogenous polynucleotide encoding a polypeptide having an amino acid sequence at least 85% homologous to SEQ ID NO: 177, 110, 113, 114, 117, 118, 120, 122, 125, 128, 129, 132, 133, 136, 139, 141, 146, 151, 158, 159, 160, 162, 163, 164, 165, 166, 167, 173, 178, 179, 182, 186, 187, 188, 189, 193, 195, 196, 202, 203, 207, 210, 211, 212, 213, 214, 215, 216, 217, 218, 1341 or 1343, thereby increasing fertilizer use efficiency and/or uptake of the plant.

According to still further features in the described preferred embodiments the expressing is effected by:

-   -   (a) transforming a cell of the plant with the exogenous         polynucleotide;     -   (b) generating a mature plant from the cell; and     -   (c) cultivating the mature plant under conditions suitable for         expressing the exogenous polynucleotide within the mature plant.

According to still further features in the described preferred embodiments the transforming is effected by introducing to the plant cell a nucleic acid construct including the exogenous polynucleotide and at least one promoter capable of directing transcription of the exogenous polynucleotide in the plant cell.

According to still further features in the described preferred embodiments the at least one promoter is a constitutive promoter.

According to further features in preferred embodiments of the invention described below, the promoter is a constitutive promoter.

According to still further features in the described preferred embodiments the constitutive promoter is CaMV 35S promoter.

According to still further features in the described preferred embodiments the promoter is an inducible promoter.

According to still further features in the described preferred embodiments the inducible promoter is an abiotic stress inducible promoter.

According to still further features in the described preferred embodiments the promoter is a tissue specific promoter.

According to still further features in the described preferred embodiments the tissue is a root tissue.

According to still further features in the described preferred embodiments the host cell is a plant cell.

According to still further features in the described preferred embodiments the plant cell forms a part of a dicotyledonous plant cell.

According to still further features in the described preferred embodiments the plant cell forms a part of a monocotyledonous plant cell.

According to still further features in the described preferred embodiments the stress condition is an abiotic stress.

According to still further features in the described preferred embodiments the abiotic stress is selected from the group consisting of salinity, drought, low temperature, high temperature, heavy metal toxicity, anaerobiosis, osmoticum, and nutrient deficiency.

According to still further features in the described preferred embodiments the nutrient is nitrogen.

According to still further features in the described preferred embodiments the plant is a dicotyledonous plant.

According to still further features in the described preferred embodiments the plant is a monocotyledonous plant.

According to still further features in the described preferred embodiments the polynucleotide comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 68, 1, 4, 5, 8, 9, 11, 13, 16, 19, 20, 23, 24, 27, 30, 32, 37, 42, 49, 50, 51, 53, 54, 55, 56, 57, 58, 64, 69, 70, 73, 77, 78, 79, 80, 84, 86, 87, 93, 94, 98, 101, 102, 103, 104, 105, 106, 107, 108, 109, 219-767, 1317, 1318, 1319, 1320, 1321, 1322, 1323, 1324, 1325, 1326, 1327, 1328, 1329, 1330, 1331, 1332, 1333, 1334, 1335, 1336, 1340 or 1342.

According to still further features in the described preferred embodiments the amino acid sequence is as set forth in SEQ ID NO: 177, 110, 113, 114, 117, 118, 120, 122, 125, 128, 129, 132, 133, 136, 139, 141, 146, 151, 158, 159, 160, 162, 163, 164, 165, 166, 167, 173, 178, 179, 182, 186, 187, 188, 189, 193, 195, 196, 202, 203, 207, 210, 211, 212, 213, 214, 215, 216, 217, 218, 768-1051, 1053-1098, 1100-1316, 1341 or 1343.

According to still further features in the described preferred embodiments the conditions are abiotic stress conditions.

According to still further features in the described preferred embodiments the conditions are fertilizer deficiency conditions.

According to still an additional aspect of the present invention there is provided a method for irrigation comprising:

-   -   (a) placing on or in a soil a dripping irrigation system so as         to obtain irrigation holes distributed 20-40 cm from one another         in the X and Y directions; and     -   (b) continuously irrigating through each of said irrigation         holes at an irrigation rate of 0.5-2 liter water per hour.

According to a further aspect of the present invention there is provided an irrigation system for mimicking drought conditions comprising:

-   -   (i) a dripping irrigation system having irrigation holes         distributed 20-40 cm from one another in the X and Y directions;         and     -   (ii) a water supply and control system for continuously         irrigating through each of said irrigation holes 0.5-2 liter         water per hour.

The present invention successfully addresses the shortcomings of the presently known configurations by providing polynucleotides and polypeptides which improve fertilizer use/uptake efficiency in transgenic plants expressing same.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

The invention is herein described, by way of example only, with reference to the accompanying drawings. With specific reference now to the drawings in detail, it is stressed that the particulars shown are by way of example and for purposes of illustrative discussion of the preferred embodiments of the present invention only, and are presented in the cause of providing what is believed to be the most useful and readily understood description of the principles and conceptual aspects of the invention. In this regard, no attempt is made to show structural details of the invention in more detail than is necessary for a fundamental understanding of the invention, the description taken with the drawings making apparent to those skilled in the art how the several forms of the invention may be embodied in practice.

In the drawings:

FIG. 1A is a schematic illustration describing the development of the plant root system in drought. Scarce soil humidity induces the formation of a deeper root system. The drawing is adapted from J E Weaver [Root Development of Field Crops. McGraw Hill Inc., New York, 291 p. (1926)].

FIG. 1B is a schematic representation of the biological strategies chosen to improve the NUE trait and the translation of the strategies to the queries performed during computational data mining.

FIGS. 2A-D show digital expression of FUE_(—)1.

FIGS. 3A-D are graphs showing expression of control genes (Nitrogen transporters and Glutamine synthase) as a function of nitrogen content in the soil. Plants were grown in 10 liter pots with increasing concentrations of either NH₄NO₃ (at 0.005, 0.05, 0.5 and 5 mM) or KNO₃ (at 0.01, 0.1, 1 or 5 mM). Plants were grown for approximately 30 days and tissues were snap frozen in liquid nitrogen. RNA was extracted from the tissues and later treated with DNAse. RNA was reverse-transcribed and used for quantification assays using Real Time PCR. For normalization, the expression at each point was divided by the geometric mean of the expression of four housekeeping as described in Example 2. The results shown are the ratio between the normalized expression and the expression levels measured at the highest concentration checked (5 mM NH₄NO₃ or 5 mM KNO₃).

FIGS. 4A-K are graphs showing correlated expression of polynucleotide sequences of the present invention with nitrogen availability.

FIGS. 5A-E are graphs showing inversely correlated expression of polynucleotide sequences of the present invention with nitrogen availability.

FIG. 6 is a schematic stepwise representation of the technology used for plant rosette area quantitation from digital images. The processing step filters the green parts of the individual plants. After designation of individual ROIs (Region of Interest) the area covered by the rosette area is calculated and exported to a worksheet.

FIGS. 7A-B are photographs showing the ability of polynucleotides of the present invention to increase nitrogen use efficiency. FIG. 7A transgenic—T1 plants expressing FUE_(—)504 (SEQ ID NO: 108) under the TT105 promoter. FIG. 7B one representative transgenic event expressing FUE_(—)43 (SEQ ID NO: 70) under the 35S promoter. Plants were grown at very limiting nitrogen conditions (0.05 and 0.2 mM combined inorganic nitrogen). Control plants (expressing a reporter gene under the same promoter or non-transgenic plants) were treated similarly. The notorious differences in plantlet size are translated into significant differences in the measured fresh weight of the plantlets.

FIG. 8 is a photograph showing transgenic plants from three independent transgenic events expressing FUE_(—)34_Evo (SEQ ID NO: 54). The plant shows impressive branching at every node as determined by a triple blind assay. The root system from the plants was also highly branched and compact (not shown).

FIG. 9 shows five independent transgenic events of plants expressing FUE_(—)40 (also termed FUE6/40, SEQ ID NO: 11). It is clearly notable that the flowering stem is unusually upright and stiff. In addition, an unusually high number of siliques can be counted. As a result, transgenic plants expressing FUE_(—)40 are remarkably prolific.

FIG. 10 a scheme of an irrigation system in accordance with the teachings of the present invention.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

The present invention is of isolated polypeptides, polynucleotides encoding same, transgenic plants expressing same and methods of using same. Specifically the present invention can be used to increase fertilizer use efficiency and stress resistance as well as biomass, vigor and yield of transgenic plants.

The principles and operation of the present invention may be better understood with reference to the drawings and accompanying descriptions.

Before explaining at least one embodiment of the invention in detail, it is to be understood that the invention is not limited in its application to the details set forth in the following description or exemplified by the Examples. The invention is capable of other embodiments or of being practiced or carried out in various ways. Also, it is to be understood that the phraseology and terminology employed herein is for the purpose of description and should not be regarded as limiting.

As the cost of Nitrogen (N) fertilizer increases and profit of crop plants production is put as risk, scientists are challenged to develop strategies that improve N use efficiency (NUE). Thus, under or over-fertilization results in a loss of profit. Lower rates of N applied result in reduced biomass as may be evidenced by reduced tillering, size, poor grain fill, reduced yields and low amino acid and protein content. Alternatively, over application of nitrogen can result in reduced yield, higher input cost and increased risk to the environment.

While reducing the present invention to practice, the present inventors uncovered through laborious bioinformatic analyses and experimentation, polynucleotide sequences and polypeptides encoded therefrom which can be used to generate transgenic plants with improved fertilizer use efficiency, stress tolerance, nutritional value (e.g., amino acids and protein content), biomass, yield and/or vigor.

As is illustrated hereinbelow and in the examples section which follows, maize polynucleotide sequences were selected based on several criteria (see Example 1 of the Examples section which follows). These included high levels of calculated digital expression at the root tips especially in water stressed roots (e.g., drought). A secondary filter for the above polynucleotide sequences was based on the digital expression of their orthologous sequences (i.e., dicotyledon plants or other monocotyledons species). Orthologous genes showing similar digital expression as the maize genes (e.g., root libraries of stress treated plants subjected) were selected. Data mining and annotation tools were used to filter genes which may have broad effects on cell metabolism. For example genes which can modify root architecture, increase nitrogen storage capacity, improve nitrogen assimilation process, and enhance the stay-green trait were selected. Those genes were finally selected for molecular validation (see Examples 3 and 9). A schematic representation of the computational filters applied to identify the polynucleotide sequences of the present invention is presented in FIG. 1B and it is provided for illustration only.

Sequences thus identified were experimentally validated. As shown in Examples 6-11 transgenic plants expressing the nucleic acid sequences of the present invention were shown to have increased fertilizer use/uptake efficiency, tolerance to abiotic stress, biomass and yield. These results strongly support the robustness of the methodology of the present invention and substantiate the use of these genes in agriculture.

Thus, according to one aspect of the present invention, there is provided a nucleic acid construct comprising a nucleic acid sequence at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% identical to a nucleotide sequence selected from the group consisting of SEQ ID NO: 68, 1, 4, 5, 8, 9, 11, 13, 16, 19, 20, 23, 24, 27, 30, 32, 37, 42, 49, 50, 51, 53, 54, 55, 56, 57, 58, 64, 69, 70, 73, 77, 78, 79, 80, 84, 86, 87, 93, 94, 98, 101, 102, 103, 104, 105, 106, 107, 108, 109, 1340 and 1342.

Nucleic acid sequences may encode polypeptide sequences comprising an amino acid sequence at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% homologous to SEQ ID NO 177, 110, 113, 114, 117, 118, 120, 122, 125, 128, 129, 132, 133, 136, 139, 141, 146, 151, 158, 159, 160, 162, 163, 164, 165, 166, 167, 173, 178, 179, 182, 186, 187, 188, 189, 193, 195, 196, 202, 203, 207, 210, 211, 212, 213, 214, 215, 216, 217, 218, 1341 or 1343.

Homology (e.g., percent homology) can be determined using any homology comparison software, including for example, the BlastP software of the National Center of Biotechnology Information (NCBI) such as by using default parameters.

Identity (e.g., percent homology) can be determined using any homology comparison software, including for example, the BlastN software of the National Center of Biotechnology Information (NCBI) such as by using default parameters.

According to one preferred embodiment of this aspect of the present invention the isolated polynucleotide is as set forth is SEQ ID NO: 68, 1, 4, 5, 8, 9, 11, 13, 16, 19, 20, 23, 24, 27, 30, 32, 37, 42, 49, 50, 51, 53, 54, 55, 56, 57, 58, 64, 69, 70, 73, 77, 78, 79, 80, 84, 86, 87, 93, 94, 98, 101, 102, 103, 104, 105, 106, 107, 108, 109, 219-767, 1317, 1318, 1319, 1320, 1321, 1322, 1323, 1324, 1325, 1326, 1327, 1328, 1329, 1330, 1331, 1332, 1333, 1334, 1335 or 1336.

A nucleic acid sequence (also termed herein as isolated polynucleotide) of the present invention refers to a single or double stranded nucleic acid sequence which is isolated and provided in the form of an RNA sequence, a complementary polynucleotide sequence (cDNA), a genomic polynucleotide sequence and/or a composite polynucleotide sequences (e.g., a combination of the above).

As used herein the phrase “complementary polynucleotide sequence” refers to a sequence, which results from reverse transcription of messenger RNA using a reverse transcriptase or any other RNA dependent DNA polymerase. Such a sequence can be subsequently amplified in vivo or in vitro using a DNA dependent DNA polymerase.

As used herein the phrase “genomic polynucleotide sequence” refers to a sequence derived (isolated) from a chromosome and thus it represents a contiguous portion of a chromosome.

As used herein the phrase “composite polynucleotide sequence” refers to a sequence, which is at least partially complementary and at least partially genomic. A composite sequence can include some exonal sequences required to encode the polypeptide of the present invention, as well as some intronic sequences interposing therebetween. The intronic sequences can be of any source, including of other genes, and typically will include conserved splicing signal sequences. Such intronic sequences may further include cis acting expression regulatory elements.

Nucleic acid sequences of the polypeptides of the present invention may be optimized for plant expression. Such optimized sequences are provided in SEQ ID NOs: 1317, 1319, 1320, 1321, 1322, 1324, 1325, 1326, 1327, 1328, 1329, 1330, 1331, 1332, 1333, 1334, 1335 and 1336. Examples of such sequence modifications include, but are not limited to, an altered G/C content to more closely approach that typically found in the plant species of interest, and the removal of codons atypically found in the plant species commonly referred to as codon optimization.

The phrase “codon optimization” refers to the selection of appropriate DNA nucleotides for use within a structural gene or fragment thereof that approaches codon usage within the plant of interest. Therefore, an optimized gene or nucleic acid sequence refers to a gene in which the nucleotide sequence of a native or naturally occurring gene has been modified in order to utilize statistically-preferred or statistically-favored codons within the plant. The nucleotide sequence typically is examined at the DNA level and the coding region optimized for expression in the plant species determined using any suitable procedure, for example as described in Sardana et al. (1996, Plant Cell Reports 15:677-681). In this method, the standard deviation of codon usage, a measure of codon usage bias, may be calculated by first finding the squared proportional deviation of usage of each codon of the native gene relative to that of highly expressed plant genes, followed by a calculation of the average squared deviation. The formula used is: 1 SDCU=n=1 N[(Xn−Yn)/Yn]2/N, where Xn refers to the frequency of usage of codon n in highly expressed plant genes, where Yn to the frequency of usage of codon n in the gene of interest and N refers to the total number of codons in the gene of interest. A table of codon usage from highly expressed genes of dicotyledonous plants is compiled using the data of Murray et al. (1989, Nuc Acids Res. 17:477-498).

One method of optimizing the nucleic acid sequence in accordance with the preferred codon usage for a particular plant cell type is based on the direct use, without performing any extra statistical calculations, of codon optimization tables such as those provided on-line at the Codon Usage Database through the NIAS (National Institute of Agrobiological Sciences) DNA bank in Japan (Hypertext Transfer Protocol://World Wide Web (dot) kazusa (dot) or (dot) jp/codon/). The Codon Usage Database contains codon usage tables for a number of different species, with each codon usage table having been statistically determined based on the data present in Genbank.

By using the above tables to determine the most preferred or most favored codons for each amino acid in a particular species (for example, rice), a naturally-occurring nucleotide sequence encoding a protein of interest can be codon optimized for that particular plant species. This is effected by replacing codons that may have a low statistical incidence in the particular species genome with corresponding codons, in regard to an amino acid, that are statistically more favored. However, one or more less-favored codons may be selected to delete existing restriction sites, to create new ones at potentially useful junctions (5′ and 3′ ends to add signal peptide or termination cassettes, internal sites that might be used to cut and splice segments together to produce a correct full-length sequence), or to eliminate nucleotide sequences that may negatively effect mRNA stability or expression.

The naturally-occurring encoding nucleotide sequence may already, in advance of any modification, contain a number of codons that correspond to a statistically-favored codon in a particular plant species. Therefore, codon optimization of the native nucleotide sequence may comprise determining which codons, within the native nucleotide sequence, are not statistically-favored with regards to a particular plant, and modifying these codons in accordance with a codon usage table of the particular plant to produce a codon optimized derivative. A modified nucleotide sequence may be fully or partially optimized for plant codon usage provided that the protein encoded by the modified nucleotide sequence is produced at a level higher than the protein encoded by the corresponding naturally occurring or native gene. Construction of synthetic genes by altering the codon usage is described in for example PCT Patent Application 93/07278.

Thus, the present invention encompasses nucleic acid sequences described hereinabove; fragments thereof, sequences hybridizable therewith, sequences homologous thereto, sequences orthologous thereto, sequences encoding similar polypeptides with different codon usage, altered sequences characterized by mutations, such as deletion, insertion or substitution of one or more nucleotides, either naturally occurring or man induced, either randomly or in a targeted fashion.

Nucleic acid sequences of the present invention may encode previously uncharacterized polypeptides

Thus the present invention provides a polypeptide having an amino acid sequence at least about 70%, at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% homologous to an amino acid sequence selected from the group consisting of SEQ ID NO: 177, 110, 113, 114, 117, 118, 120, 122, 125, 128, 129, 132, 133, 136, 139, 141, 146, 151, 158, 159, 160, 162, 163, 164, 165, 166, 167, 173, 178, 179, 182, 186, 187, 188, 189, 193, 195, 196, 202, 203, 207, 210, 211, 212, 213, 214, 215, 216, 217, 218, 1341 or 1343.

According to an embodiment of this aspect of the present invention the isolated polypeptide comprises an amino acid sequence selected from the group consisting of 177, 110, 113, 114, 117, 118, 120, 122, 125, 128, 129, 132, 133, 136, 139, 141, 146, 151, 158, 159, 160, 162, 163, 164, 165, 166, 167, 173, 178, 179, 182, 186, 187, 188, 189, 193, 195, 196, 202, 203, 207, 210, 211, 212, 213, 214, 215, 216, 217, 218, 768-1051, 1053-1098, 1100-1315, 1316, 1341 or 1343.

The present invention also encompasses sequences homologous and orthologous to the above mentioned polypeptides, fragments of the above described polypeptides and polypeptides having mutations, such as deletions, insertions or substitutions of one or more amino acids, either naturally occurring or man induced, either randomly or in a targeted fashion.

Polynucleotides and polypeptides of the present invention are used for plant expression.

The term “plant” as used herein encompasses whole plants, ancestors and progeny of the plants and plant parts, including seeds, shoots, stems, roots (including tubers), and plant cells, tissues and organs. The term “plant” also therefore encompasses suspension cultures, embryos, meristematic regions, callus tissue, leaves, gametophytes, sporophytes, pollen, and microspores. Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants which are of commercial value, including a fodder or forage legume, ornamental plant, food crop, tree, or shrub selected from the following non-limiting list comprising Acacia spp., Acer spp., Actinidia spp., Aesculus spp., Agathis australis, Albizia amara, Alsophila tricolor, Andropogon spp., Arachis spp, Areca catechu, Astelia fragrans, Astragalus cicer, Baikiaea plurijuga, Betula spp., Brassica spp., Bruguiera gymnorrhiza, Burkea africana, Butea frondosa, Cadaba farinosa, Calliandra spp, Camelia sinensis, Canna indica, Capsicum spp., Cassia spp., Cent roema pubescens, Chaenomeles spp., Cinnamomum cassia, Coffea arabica, Colophospermum mopane, Coronillia varia, Cotoneaster serotina, Crataegus spp., Cucumis spp., Cupressus spp., Cyathea dealbata, Cydonia oblonga, Ciyptomeria laponica, Cymbopogon spp., Cynthea dealbata, Cydonia oblonga, Dalbergia monetaria, Davalila divaricata, De smodium spp., Dicksonia squarosa, Diheteropogon amplectens, Dioclea spp, Dolichos spp., Doiycnium rectum, Echinochloa pyramidalis, Ehrartia spp., Eleusine coracana, Era grestis spp., Erythrina spp., Eucalyptus spp, Euclea. schimpen Eulalia villosa, Fagopyrum spp., Felloa sellowiana, Fragaria spp., Flemingia spp, Freycinetia banksii, Geranium thunbergi, Ginkgo biloba, Glycine javanica, Gliricidia spp, Gossypium hirsutum, Gre villea spp., Guibourtia coleosperma, Hedysarum spp., Hemarthia altissima, Heteropogon con tortus, Hordeum vulgare, Hyparrhenia rufa, Hypericum erectum, Hyperthelia dissoluta, Indigo incarnata, Iris spp., Jatropha curcas, Leptarrhena pyrolifolia, Lespediza spp., Lettuca spp., Leucaena leucocephala, Loudetia simplex, Lotonus bainesi, Lotus spp., Macrotyloma axifiare, Malus spp., Manihot esculenta, Medicago sativa, Metasequoia glyptostroboides, Musa sapientum, Nicotianum spp., Onobtychis spp., Ornithopus spp., Oryza spp., Peltophorum african urn, Pennisetum spp., Persea gratissima, Petunia spp., Phaseolus spp., Phoenix canariensis, Phormium cookianum, Photinia spp., Picea glauca, Pinus spp., Pisum sativum, Podocarpus totara, Pogonarthria flecki, Pogonarthria squarrosa, Populus spp., Prosopis cineraria, Pseudotsuga menziesi, Pterolobium stellatum, Pyrus communis, Quercus spp., Rhaphiolepsis umbellata, Rhopalostylis sapida, Rhu.s natalensis, Ribes grossularia, Ribes spp., Robinia pseudoacacia, Rosa spp., Rub us spp., Salix spp., Schyzachyrium sanguineurn, Sciadopitys verticillata, Sequoia sempen'irens, Sequoiadendron giganteum, Sorghum bicolor, Spinacia spp., Sporobolus fimbriatus, Stiburus alopecuroides, Stylosanthos humilis, Tadehagi spp, Taxodium distichum, Themeda triandra, Trifollum spp., Triticum spp., Tsuga heterophylla, Vaccinium spp., Vicia spp., Vitis vinifera, Watsonia pyramidata, Zantedeschia aethiopica, Zea mays, amaranth, artichoke, asparagus, broccoli, Brussels sprouts, cabbage, canola, carrot, cauliflower, celery, collard greens, flax, kale, lentil, ollseed rape, okra, onion, potato, rice, soybean, straw, sugar beet, sugar cane, sunflower, tomato, squash tea, trees. Alternatively algae and other non-Viridiplantae can be used.

Expressing the exogenous polynucleotide of the present invention within the plant can be effected by transforming one or more cells of the plant with the exogenous polynucleotide, followed by generating a mature plant from the transformed cells and cultivating the mature plant under conditions suitable for expressing the exogenous polynucleotide within the mature plant.

Preferably, the transformation is effected by introducing to the plant cell a nucleic acid construct which includes the exogenous polynucleotide of the present invention and at least one promoter capable of directing transcription of the exogenous polynucleotide in the plant cell. Further details of suitable transformation approaches are provided hereinbelow.

As used herein, the term “promoter” refers to a region of DNA which lies upstream of the transcriptional initiation site of a gene to which RNA polymerase binds to initiate transcription of RNA. The promoter controls where (e.g., which portion of a plant, which organ within an animal, etc.) and/or when (e.g., which stage or condition in the lifetime of an organism) the gene is expressed.

Any suitable promoter sequence can be used by the nucleic acid construct of the present invention. The following types of promoters are non-limiting examples of promoters used to over-express the selected genes: general promoters, root specific promoters, root-tips specific promoters, drought-induced root promoters, biotic stress-induced promoters, abiotic stress-induced promoters, nitrogen induced promoters, ammonium or nitrate induced promoters, phosphate fertilizer-induced promoters, leaf specific promoters, inducible promoters, constitutive promoters, promoters with two or more of the characteristics described above, or other novel promoters.

Choice of the promoter is based largely on the phenotype of interest and is determined by such factors as tissue (e.g., seed, fruit, root, pollen, vascular tissue, flower, carpel, etc.), inducibility (e.g., in response to wounding, heat, cold, drought, light, pathogens, etc.), timing, developmental stage, and the like. Numerous known promoters have been characterized and can favorably be employed to promote expression of a polynucleotide of the invention in a transgenic plant or cell of interest. Measures should be taken, however, to select a promoter which will mediate desirable expression levels of the transgene so as to avoid reallocating excessive energetic resources which may affect final yield, strength, mass and lodging and incidence of foliar pathogens. This should also be viewed from an economic perspective.

Suitable constitutive promoters include, for example, CaMV 35S promoter (SEQ ID NO: 1337; Odell et al., Nature 313:810-812, 1985); Arabidopsis At6669 promoter (SEQ ID NO: 1514, PCT No WO2004/104162); TT105 (SEQ ID NO: 1339, PCT NO.: WO2004/081173) maize Ubi 1 (Christensen et al., Plant Sol. Biol. 18:675-689, 1992); rice actin (McElroy et al., Plant Cell 2:163-171, 1990); pEMU (Last et al., Theor. Appl. Genet. 81:581-588, 1991); and Synthetic Super MAS (Ni et al., The Plant Journal 7: 661-76, 1995). Other constitutive promoters include those in U.S. Pat. Nos. 5,659,026, 5,608,149; 5,608,144; 5,604,121; 5,569,597: 5,466,785; 5,399,680; 5,268,463; and 5,608,142.

Suitable tissue-specific promoters include, but not limited to, leaf-specific promoters such as described, for example, by Yamamoto et al., Plant J. 12:255-265, 1997; Kwon et al., Plant Physiol. 105:357-67, 1994; Yamamoto et al., Plant Cell Physiol. 35:773-778, 1994; Gotor et al., Plant J. 3:509-18, 1993; Orozco et al., Plant Mol. Biol. 23:1129-1138, 1993; and Matsuoka et al., Proc. Natl. Acad. Sci. USA 90:9586-9590, 1993. Especially preferred are root promoters such as the ROOTP promoter [SEQ ID NO: 1338; Upstream region of the gene ATXTH19 (AT4G30290, Xyloglucan endotransglucosylase/hydrolase 19, described in Vissenberg K, et al. Plant Cell Physiol. 2005 January; 46(1):192-200].

A variety of plant gene promoters are known to regulate gene expression in response to environmental, hormonal, chemical, developmental signals, and in a tissue-active manner. Examples of seed-specific promoters (such as the napin, phaseolin or DC3 promoter described in U.S. Pat. No. 5,773,697), fruit-specific promoters that are active during fruit ripening, such as the dru 1 promoter (U.S. Pat. No. 5,783,393), or the 2A11 promoter (U.S. Pat. No. 4,943,674) and the tomato polygalacturonase promoter (Bird et al. (1988) Plant Mol. Biol. 11: 651-662), root-specific promoters, such as ARSK1, and those disclosed in U.S. Pat. Nos. 5,618,988, 5,837,848 and 5,905,186, epidermis-specific promoters, including CUT1 (Kunst et al. (1999) Biochem. Soc. Tians. 28: 651-654), pollen-active promoters such as PTA29, PTA26 and PTA 13 (U.S. Pat. No. 5,792,929), promoters active in vascular tissue (Ringli and Keller (1998) Plant Mol. Biol. 37: 977-988), flower-specific (Kaiser et al. (1995) Plant Mol. Biol. 28: 231-243), pollen (Baerson et al. (1994) Plant Mol. Biol. 26: 1947-1959), carpels (Ohl et al. (1990) Plant Cell 2: 837-848), pollen and ovules (Baerson et al. (1993) Plant Mol. Biol. 22: 255-267), auxin-inducible promoters (such as that described in van der Kop et al. (1999) Plant Mol. Biol. 39: 979-990 or Baumann et al. (1999) Plant Cell 11: 323-334), cytokinin-inducible promoter (Guevara-Garcia (1998) Plant Mol. Biol. 38: 743-753), promoters responsive to gibberellin (Shi et al. (1998) Plant Mol. Biol. 38: 1053-1060, Willmott et al. (1998) Plant Mol. Biol. 38: 817-825) and the like. Additional promoters are those that elicit expression in response to heat (Ainley et al. (1993) Plant Mol. Biol. 22: 13-23), light (e.g., the pea rbcS-3A promoter, described in Kuhlemeier et al. (1989) Plant Cell 1: 471-478, and the maize rbcS promoter, described in Schaffier and Sheen (1991) Plant Cell 3: 997-1012); wounding (e.g., wunl, described in Siebertz et al. (1989) Plant Cell 1: 961-968), pathogens (such as the PR-1 promoter described in Buchel et al. (1999) Plant Mol. Biol. 40: 387-396, and the PDF1.2 promoter described in Manners et al. (1998) Plant Mol. Biol. 38: 1071-1080), and chemicals such as methyl jasmonate or salicylic acid (Gatz (1997) Annu. Rev. Plant Physiol. Plant Mol. Biol. 48: 89-108). In addition, the timing of the expression can be controlled by using promoters such as those acting at senescence (Gan and Amasino (1995) Science 270: 1986-1988); or late seed development (Odell et al. (1994) Plant Physiol. 106: 447-458).

Other examples of promoters are a SUC2 promoter (Truernit and Sauer, Planta. (1995) 196:564-70), and a stress-inducible promoter such as RD29A (Yamaguchi-Shinozaki and Shinozaki K. Plant Cell (1994) 6:251-264), promoters fro the PlantProm database (Shahmuradov et al. Nucleic Acids Res. (2003) 31:114-7), the rice CatB promoter (Iwamoto et al. Plant Physiol Biochem. (2004) 42:241-9), the root specific and phosphate-deficiency inducible barley promoters of the phosphate transporter gene family (HvPht1;1 and HvPht1;2) (Schunmann et al. (2004); 55:855-65), tissue specific and constitutive promoters illustrated in patent No: WO2004/081173, in U.S. Pat. No. 5,633,363, in patent No: WO 2000/15662, in patent No: WO 2004/013169, in patent No: US 2005/010974, in patent No: WO 2005/035770, in patent No: US 2001/0047525, in U.S. Pat. No. 5,837,848, in U.S. Pat. No. 6,018,099, etc.

The nucleic acid construct of the present invention preferably further includes an appropriate selectable marker and/or an origin of replication. Preferably, the nucleic acid construct utilized is a shuttle vector, which can propagate both in E. coli (wherein the construct comprises an appropriate selectable marker and origin of replication) and be compatible with propagation in cells. The construct according to the present invention can be, for example, a plasmid, a bacmid, a phagemid, a cosmid, a phage, a virus or an artificial chromosome.

The nucleic acid construct of the present invention can be utilized to stably or transiently transform plant cells. In stable transformation, the exogenous polynucleotide of the present invention is integrated into the plant genome and as such it represents a stable and inherited trait. In transient transformation, the exogenous polynucleotide is expressed by the cell transformed but it is not integrated into the genome and as such it represents a transient trait.

There are various methods of introducing foreign genes into both monocotyledonous and dicotyledonous plants (Potrykus, I., Annu. Rev. Plant. Physiol., Plant. Mol. Biol. (1991) 42:205-225; Shimamoto et al., Nature (1989) 338:274-276).

The principle methods of causing stable integration of exogenous DNA into plant genomic DNA include two main approaches:

(i) Agrobacterium-mediated gene transfer: Klee et al. (1987) Annu. Rev. Plant Physiol. 38:467-486; Klee and Rogers in Cell Culture and Somatic Cell Genetics of Plants, Vol. 6, Molecular Biology of Plant Nuclear Genes, eds. Schell, J., and Vasil, L. K., Academic Publishers, San Diego, Calif. (1989) p. 2-25; Gatenby, in Plant Biotechnology, eds. Kung, S, and Arntzen, C. J., Butterworth Publishers, Boston, Mass. (1989) p. 93-112.

(ii) Direct DNA uptake: Paszkowski et al., in Cell Culture and Somatic Cell Genetics of Plants, Vol. 6, Molecular Biology of Plant Nuclear Genes eds. Schell, J., and Vasil, L. K., Academic Publishers, San Diego, Calif. (1989) p. 52-68; including methods for direct uptake of DNA into protoplasts, Toriyama, K. et al. (1988) Bio/Technology 6:1072-1074. DNA uptake induced by brief electric shock of plant cells: Zhang et al. Plant Cell Rep. (1988) 7:379-384. Fromm et al. Nature (1986) 319:791-793. DNA injection into plant cells or tissues by particle bombardment, Klein et al. Bio/Technology (1988) 6:559-563; McCabe et al. Bio/Technology (1988) 6:923-926; Sanford, Physiol. Plant. (1990) 79:206-209; by the use of micropipette systems: Neuhaus et al., Theor. Appl. Genet. (1987) 75:30-36; Neuhaus and Spangenberg, Physiol. Plant. (1990) 79:213-217; glass fibers or silicon carbide whisker transformation of cell cultures, embryos or callus tissue, U.S. Pat. No. 5,464,765 or by the direct incubation of DNA with germinating pollen, DeWet et al. in Experimental Manipulation of Ovule Tissue, eds. Chapman, G. P. and Mantell, S. H. and Daniels, W. Longman, London, (1985) p. 197-209; and Ohta, Proc. Natl. Acad. Sci. USA (1986) 83:715-719.

The Agrobacterium system includes the use of plasmid vectors that contain defined DNA segments that integrate into the plant genomic DNA. Methods of inoculation of the plant tissue vary depending upon the plant species and the Agrobacterium delivery system. A widely used approach is the leaf disc procedure which can be performed with any tissue explant that provides a good source for initiation of whole plant differentiation. Horsch et al. in Plant Molecular Biology Manual A5, Kluwer Academic Publishers, Dordrecht (1988) p. 1-9. A supplementary approach employs the Agrobacterium delivery system in combination with vacuum infiltration. The Agrobacterium system is especially viable in the creation of transgenic dicotyledonous plants.

There are various methods of direct DNA transfer into plant cells. In electroporation, the protoplasts are briefly exposed to a strong electric field. In microinjection, the DNA is mechanically injected directly into the cells using very small micropipettes. In microparticle bombardment, the DNA is adsorbed on microprojectiles such as magnesium sulfate crystals or tungsten particles, and the microprojectiles are physically accelerated into cells or plant tissues.

Following stable transformation plant propagation is exercised. The most common method of plant propagation is by seed. Regeneration by seed propagation, however, has the deficiency that due to heterozygosity there is a lack of uniformity in the crop, since seeds are produced by plants according to the genetic variances governed by Mendelian rules. Basically, each seed is genetically different and each will grow with its own specific traits. Therefore, it is preferred that the transformed plant be produced such that the regenerated plant has the identical traits and characteristics of the parent transgenic plant. Therefore, it is preferred that the transformed plant be regenerated by micropropagation which provides a rapid, consistent reproduction of the transformed plants.

Micropropagation is a process of growing new generation plants from a single piece of tissue that has been excised from a selected parent plant or cultivar. This process permits the mass reproduction of plants having the preferred tissue expressing the fusion protein. The new generation plants which are produced are genetically identical to, and have all of the characteristics of, the original plant. Micropropagation allows mass production of quality plant material in a short period of time and offers a rapid multiplication of selected cultivars in the preservation of the characteristics of the original transgenic or transformed plant. The advantages of cloning plants are the speed of plant multiplication and the quality and uniformity of plants produced.

Micropropagation is a multi-stage procedure that requires alteration of culture medium or growth conditions between stages. Thus, the micropropagation process involves four basic stages: Stage one, initial tissue culturing; stage two, tissue culture multiplication; stage three, differentiation and plant formation; and stage four, greenhouse culturing and hardening. During stage one, initial tissue culturing, the tissue culture is established and certified contaminant-free. During stage two, the initial tissue culture is multiplied until a sufficient number of tissue samples are produced to meet production goals. During stage three, the tissue samples grown in stage two are divided and grown into individual plantlets. At stage four, the transformed plantlets are transferred to a greenhouse for hardening where the plants' tolerance to light is gradually increased so that it can be grown in the natural environment.

Preferably, mature transformed plants generated as described above are further selected for the trait of interest (e.g., improved FUE, stress tolerance etc.). Examples of such screening assays are provided hereinbelow and in the Examples section which follows. Thus, for example, transgenic plants may be screened for improved nutritional value (e.g., improved oil, amino acids and/or protein content, as well as N content per se) under normal or stress conditions as will be further described hereinbelow. Alternatively or additionally, transformed and non-transformed (wild type) plants are exposed to an abiotic stress condition, such as water depravation, suboptimal temperature, nutrient deficiency, or preferably a salt stress condition. Salt stress can be effected in many ways such as, for example, by irrigating the plants with a hyperosmotic solution, by cultivating the plants hydroponically in a hyperosmotic growth solution (e.g., Hoagland solution), or by culturing the plants in a hyperosmotic growth medium (e.g., MS medium). Since different plants vary considerably in their tolerance to salinity, the salt concentration in the irrigation water, growth solution, or growth medium is preferably adjusted according to the specific characteristics of the specific plant cultivar or variety, so as to inflict a mild or moderate effect on the physiology and/or morphology of the plants (for guidelines as to appropriate concentration please see, Bernstein and Kafkafi, Root Growth Under Salinity Stress In: Plant Roots, The Hidden Half 3rd ed. Waisel Y, Eshel A and Kafkafi U. (editors) Marcel Dekker Inc., New York, 2002, and reference therein). Following exposure to the stress condition the plants are frequently monitored until substantial physiological and/or morphological effects appear in wild type plants. Subsequently, transformed plants not exhibiting substantial physiological and/or morphological effects, or exhibiting higher biomass than wild-type plants, are identified as abiotic stress tolerant plants.

Although stable transformation is presently preferred, transient transformation of leaf cells, meristematic cells or the whole plant is also envisaged by the present invention.

Transient transformation can be effected by any of the direct DNA transfer methods described above or by viral infection using modified plant viruses.

Viruses that have been shown to be useful for the transformation of plant hosts include CaMV, TMV and BV. Transformation of plants using plant viruses is described in U.S. Pat. No. 4,855,237 (BGV), EP-A 67,553 (TMV), Japanese Published Application No. 63-14693 (TMV), EPA 194,809 (BV), EPA 278,667 (BV); and Gluzman, Y. et al., Communications in Molecular Biology: Viral Vectors, Cold Spring Harbor Laboratory, New York, pp. 172-189 (1988). Pseudovirus particles for use in expressing foreign DNA in many hosts, including plants, is described in WO 87/06261.

Preferably, the virus of the present invention is avirulent and thus is incapable of causing severe symptoms such as reduced growth rate, mosaic, ring spots, leaf roll, yellowing, streaking, pox formation, tumor formation and pitting. A suitable avirulent virus may be a naturally occurring avirulent virus or an artificially attenuated virus. Virus attenuation may be effected by using methods well known in the art including, but not limited to, sub-lethal heating, chemical treatment or by directed mutagenesis techniques such as described, for example, by Kurihara and Watanabe (Molecular Plant Pathology 4:259-269, 2003), Gal-on et al. (1992), Atreya et al. (1992) and Huet et al. (1994).

Suitable virus strains can be obtained from available sources such as, for example, the American Type culture Collection (ATCC) or by isolation from infected plants. Isolation of viruses from infected plant tissues can be effected by techniques well known in the art such as described, for example by Foster and Tatlor, Eds. “Plant Virology Protocols: From Virus Isolation to Transgenic Resistance (Methods in Molecular Biology (Humana Pr), Vol 81)”, Humana Press, 1998. Briefly, tissues of an infected plant believed to contain a high concentration of a suitable virus, preferably young leaves and flower petals, are ground in a buffer solution (e.g., phosphate buffer solution) to produce a virus infected sap which can be used in subsequent inoculations.

Construction of plant RNA viruses for the introduction and expression of non-viral exogenous polynucleotide sequences in plants is demonstrated by the above references as well as by Dawson, W. O. et al., Virology (1989) 172:285-292; Takamatsu et al. EMBO J. (1987) 6:307-311; French et al. Science (1986) 231:1294-1297; and Takamatsu et al. FEBS Letters (1990) 269:73-76.

When the virus is a DNA virus, suitable modifications can be made to the virus itself. Alternatively, the virus can first be cloned into a bacterial plasmid for ease of constructing the desired viral vector with the foreign DNA. The virus can then be excised from the plasmid. If the virus is a DNA virus, a bacterial origin of replication can be attached to the viral DNA, which is then replicated by the bacteria. Transcription and translation of this DNA will produce the coat protein which will encapsidate the viral DNA. If the virus is an RNA virus, the virus is generally cloned as a cDNA and inserted into a plasmid. The plasmid is then used to make all of the constructions. The RNA virus is then produced by transcribing the viral sequence of the plasmid and translation of the viral genes to produce the coat protein(s) which encapsidate the viral RNA.

Construction of plant RNA viruses for the introduction and expression in plants of non-viral exogenous polynucleotide sequences such as those included in the construct of the present invention is demonstrated by the above references as well as in U.S. Pat. No. 5,316,931.

In one embodiment, a plant viral polynucleotide is provided in which the native coat protein coding sequence has been deleted from a viral polynucleotide, a non-native plant viral coat protein coding sequence and a non-native promoter, preferably the subgenomic promoter of the non-native coat protein coding sequence, capable of expression in the plant host, packaging of the recombinant plant viral polynucleotide, and ensuring a systemic infection of the host by the recombinant plant viral polynucleotide, has been inserted. Alternatively, the coat protein gene may be inactivated by insertion of the non-native polynucleotide sequence within it, such that a protein is produced. The recombinant plant viral polynucleotide may contain one or more additional non-native subgenomic promoters. Each non-native subgenomic promoter is capable of transcribing or expressing adjacent genes or polynucleotide sequences in the plant host and incapable of recombination with each other and with native subgenomic promoters. Non-native (foreign) polynucleotide sequences may be inserted adjacent the native plant viral subgenomic promoter or the native and a non-native plant viral subgenomic promoters if more than one polynucleotide sequence is included. The non-native polynucleotide sequences are transcribed or expressed in the host plant under control of the subgenomic promoter to produce the desired products.

In a second embodiment, a recombinant plant viral polynucleotide is provided as in the first embodiment except that the native coat protein coding sequence is placed adjacent one of the non-native coat protein subgenomic promoters instead of a non-native coat protein coding sequence.

In a third embodiment, a recombinant plant viral polynucleotide is provided in which the native coat protein gene is adjacent its subgenomic promoter and one or more non-native subgenomic promoters have been inserted into the viral polynucleotide. The inserted non-native subgenomic promoters are capable of transcribing or expressing adjacent genes in a plant host and are incapable of recombination with each other and with native subgenomic promoters. Non-native polynucleotide sequences may be inserted adjacent the non-native subgenomic plant viral promoters such that the sequences are transcribed or expressed in the host plant under control of the subgenomic promoters to produce the desired product.

In a fourth embodiment, a recombinant plant viral polynucleotide is provided as in the third embodiment except that the native coat protein coding sequence is replaced by a non-native coat protein coding sequence.

The viral vectors are encapsidated by the coat proteins encoded by the recombinant plant viral polynucleotide to produce a recombinant plant virus. The recombinant plant viral polynucleotide or recombinant plant virus is used to infect appropriate host plants. The recombinant plant viral polynucleotide is capable of replication in the host, systemic spread in the host, and transcription or expression of foreign gene(s) (exogenous polynucleotide) in the host to produce the desired protein.

Techniques for inoculation of viruses to plants may be found in Foster and Taylor, eds. “Plant Virology Protocols: From Virus Isolation to Transgenic Resistance (Methods in Molecular Biology (Humana Pr), Vol 81)”, Humana Press, 1998; Maramorosh and Koprowski, eds. “Methods in Virology” 7 vols, Academic Press, New York 1967-1984; Hill, S. A. “Methods in Plant Virology”, Blackwell, Oxford, 1984; Walkey, D. G. A. “Applied Plant Virology”, Wiley, New York, 1985; and Kado and Agrawa, eds. “Principles and Techniques in Plant Virology”, Van Nostrand-Reinhold, New York.

In addition to the above, the polynucleotide of the present invention can also be introduced into a chloroplast genome thereby enabling chloroplast expression.

A technique for introducing exogenous polynucleotide sequences to the genome of the chloroplasts is known. This technique involves the following procedures. First, plant cells are chemically treated so as to reduce the number of chloroplasts per cell to about one. Then, the exogenous polynucleotide is introduced via particle bombardment into the cells with the aim of introducing at least one exogenous polynucleotide molecule into the chloroplasts. The exogenous polynucleotides selected such that it is integratable into the chloroplast's genome via homologous recombination which is readily effected by enzymes inherent to the chloroplast. To this end, the exogenous polynucleotide includes, in addition to a gene of interest, at least one polynucleotide stretch which is derived from the chloroplast's genome. In addition, the exogenous polynucleotide includes a selectable marker, which serves by sequential selection procedures to ascertain that all or substantially all of the copies of the chloroplast genomes following such selection will include the exogenous polynucleotide. Further details relating to this technique are found in U.S. Pat. Nos. 4,945,050; and 5,693,507 which are incorporated herein by reference. A polypeptide can thus be produced by the protein expression system of the chloroplast and become integrated into the chloroplast's inner membrane.

Since the traits of the present invention (e.g., NUE and abiotic stress tolerance) in plants can involve multiple genes acting additively or in synergy (see, for example, in Quesda et al., Plant Physiol. 130:951-063, 2002), the present invention also envisages expressing a plurality of exogenous polynucleotides in a single host plant to thereby achieve superior NUE, tolerance, biomass and/or yield.

Expressing a plurality of exogenous polynucleotides in a single host plant can be effected by co-introducing multiple nucleic acid constructs, each including a different exogenous polynucleotide, into a single plant cell. The transformed cell can than be regenerated into a mature plant using the methods described hereinabove.

Alternatively, expressing a plurality of exogenous polynucleotides in a single host plant can be effected by co-introducing into a single plant-cell a single nucleic-acid construct including a plurality of different exogenous polynucleotides. Such a construct can be designed with a single promoter sequence which can transcribe a polycistronic message including all the different exogenous polynucleotide sequences. To enable co-translation of the different polypeptides encoded by the polycistronic message, the polynucleotide sequences can be inter-linked via an internal ribosome entry site (IRES) sequence which facilitates translation of polynucleotide sequences positioned downstream of the IRES sequence. In this case, a transcribed polycistronic RNA molecule encoding the different polypeptides described above will be translated from both the capped 5′ end and the two internal IRES sequences of the polycistronic RNA molecule to thereby produce in the cell all different polypeptides. Alternatively, the construct can include several promoter sequences each linked to a different exogenous polynucleotide sequence.

The plant cell transformed with the construct including a plurality of different exogenous polynucleotides, can be regenerated into a mature plant, using the methods described hereinabove.

Alternatively, expressing a plurality of exogenous polynucleotides in a single host plant can be effected by introducing different nucleic acid constructs, including different exogenous polynucleotides, into a plurality of plants. The regenerated transformed plants can then be cross-bred and resultant progeny selected for superior traits such as NUE, abiotic stress tolerance and/or biomass, using conventional plant breeding techniques.

As mentioned hereinabove, transgenic plants of the present invention can be used for improving myriad of commercially desired traits which are all interrelated as is discussed hereinbelow.

As used herein the term “trait” refers to a characteristic or quality of a plant which may overall (either directly or indirectly) improve the commercial value of the plant.

As used herein the term “improving” or “increasing” refers to improving or increasing the trait of the transgenic plant of the present invention by at least about 2% more, 5% more, 10% more, 20% more, 30% more, 40% more, 50% more, 60% more, 70% more, 80% more, 90% or more than that of the non-transgenic plant (e.g., mock transfected, or naïve).

The following are illustrative examples of traits which can be improved using the polynucleotides or polypeptides of the present invention.

Fertilizer Use Efficiency—

Although the following will be more elaborated regarding Nitrogen (N) Use Efficiency (NUE) it is to be understood that the present invention envisages increasing/improving the overall fertilizer use efficiency of all minerals and organic moieties absorbed from the soil, such as phosphates (PUE) and potassium (KUE) by the transgenic plants of the present invention.

The efficiency by which N is used by the plant is affected among other things by both N uptake efficiency and N utilization efficiency. The ratio of the amount of N uptake by the plant (or N content, kg N) over the amount of N supplied/applied (kg N_(s)) is an uptake efficiency (kg N kg⁻¹ N_(s)), while the grain yield (kg grain) to N uptake (kg N) ratio is N utilization efficiency (NUE, kg grain kg⁻¹ N). See Moll 1982 Analysis and interpretation of factors which contribute to efficiency of nitrogen utilization. Argon. J. 74:562-564. NUE is also affected by N losses through ammonia volatilization, nitrification-denitrification, leaching and runoff which decrease the availability of N to the plant.

The present inventors realized that genes which alter root architecture can be used to improve NUE. The rationale is to position a higher fraction of the roots in deeper soil layers where the fertilizer is leached or increasing the soil coverage where the fertilizer is concentrated. This strategy was already proven successful with Phosphorous deficiency in soybean (Miller, C R, I Ochoa, K L Nielsen, D Beck, J P Lynch. 2003. Genetic variation for adventitious rooting in response to low phosphorus availability: potential utility for phosphorus acquisition from stratified soils. Functional Plant Biology 30:973-985) and maize (Zhu, J, JP Lynch. 2004. The contribution of lateral rooting to phosphorus acquisition efficiency in maize (Zea mays L.) seedlings. Functional Plant Biology 31:949-958) and other crop plants. Root morphogenesis is dramatically affected by development programming as well as by environmental conditions. Drought leads to a pronounced downward development of the root structure to reach water located in deeper soil layers (see FIG. 1A) while local nutrient availability causes a local root outgrowth increasing the total absorptive surface of the root system. The development of root systems is usually highly asymmetric and reflects the ability of roots to adjust their growth and development to environmental factors. Genes and gene expression control the developmental changes, as is the case of ANR1: a putative transcription factor with a role in NO₃ ⁻ signaling. When ANR1 is down-regulated by antisense or co-suppression, the resulting transgenic lines are defective in their root response to localized supplies of NO₃ ⁻ (Zhang, H., Forde, B. G. 1998, An Arabidopsis MADS box gene that controls nutrient-induced changes in root architecture, Science 270:407). Hence, altering expression of the polynucleotides of the present invention in transgenic plants may have desirable effects on root morphogenesis, some of them could positively affect NUE and abiotic/biotic stress tolerance and/or to enhance plant yield and vigor. Specific examples include FUE_(—)7, FUE_(—)16 and FUE_(—)34_Evo.

Additionally selected are those which enhance intracellular storage reduce the cytosolic concentration, thereby reducing the energetic barrier for the membrane transporters responsible for the uptake of the different forms of the fertilizer. In this way, higher rates of fertilizer uptake can be obtained. Similarly, as expected from any enzymatic reaction or pathway, if the product of fertilizer assimilation is efficiently removed for the cellular milieu the enzymatic pathway building this product is expected to occur at accelerated rate leading to improved assimilation or use efficiency.

In yet another approach to improve FUE, a third group of genes was identified. Those genes are related to the biochemical pathways involved in the conversion of the inorganic fertilizer form to the organic material (assimilation process). Releasing bottlenecks in the assimilation process has granted promising effects on enhanced nutrients use efficiency, as in the case of the transcription factor Dof1 (Yanagisawa Sd, Akiyama A, Kisaka H, Uchimiya H, Miwa T. Metabolic engineering with Dof1 transcription factor in plants: Improved nitrogen assimilation and growth under low-nitrogen conditions. Proc Natl Acad Sci USA. 2004 May 18; 101(20):7833-8). The genes found using this approach relieve the biochemical bottlenecks leading to enhanced fertilizer use efficiency. FUE_(—)101 and FUE_(—)102 comprise a transporter activity and therefore may be used to improve nutrient uptake.

Storage Capacity—

polynucleotide and polypeptide sequences of the present invention are directed to enhance the general storage capability of the plant. The capacity for grain production is predetermined by the plants ability to absorb and store mineral nitrogen in its early phases of development (Hirel et el. Plant Physiol, March 2001, Vol. 125, pp. 1258-1270). Therefore enhanced storage capacity in the form of nitrate or amino acids highly likely will increase the grain yield. This invention includes molecular mechanisms to improve the nitrogen or any metabolic nutrient storage capacity of the plant. Examples include, amino acids, protein, starch and oil, fiber, ash, chlorophyll and mineral content.

Plant protein content is directly related to the N concentration in the grain (see Mosse 1990 J. Agric. Food Chem. 38:18-24). This is highly valuable for improving the nutritional value of food. For example, children consuming high-protein (10%_ milled rice showed improved growth compared with children consuming average-protein (6-7%) milled rice [Juliano (1993) Rice in Human Nutrition. IRRI and FAO, Rome]. Thus, transgenic plants displaying high efficiency in remobilizing N from vegetative parts to the edible part (e.g., grain) are highly valuable. Since the levels of nitrogen at flowering determine the grain yield, overexpression of the polynucleotide sequences of the present invention will improve the grain yield and/or enhance protein content of grain at the entire plant level. In addition, increased solute content of the plant prevents evaporation and water loss due to heat, drought, salinity, osmoticum, etc therefore providing a better plant tolerance to the above stresses. Overexpression of FUE_(—)501, FUE_(—)502, FUE_(—)503, FUE_(—)504 or FUE_(—)49, FUE_(—)51, FUE_(—)52, FUE_(—)53 or FUE_(—)100 and FUE_(—)101 are expected to increase the storage capacity of the tissues where they are expressed. This may lead to a stronger sink capacity, and to a better use of the fertilizer applied (particularly nitrogen) due to enhanced absorption from the soil. Since the levels of nitrogen at flowering determine the grain yield, it is expected that the overexpression of the above genes will also improve the grain yield and/or enhance protein content of grain and the entire plant protein level. In addition, increased solute content of the plant will prevent evaporation and water loss due to heat, drought, salinity, osmoticum, and the like thereby providing a better plant tolerance to the above stresses.

Delayed Leaf Senescence or “Stay-Green”—

extends nutrient uptake longer into the plant cycle providing increased capacity to store nitrogen and to provide photosynthate during grain filling. If a plant has more green leaves at the period of pollination more nitrogen will be available for redistribution to the kernels causing an improvement in fertilizer use efficiency and probably grain yield. Some of the genes presented in this invention increase the “stay green” trait or exhibit enhanced growth (faster growth and/or bigger leaves and stalks) as a mechanism to improve fertilizer use efficiency, grain yield and overall stress tolerance of the plant.

Invertase is an enzyme that is known to delay senescence when expressed under a senescence-activated promoter (Balibrea Lara, et al. Plant Cell 16: 1276-1287, 2004). FUE_(—)30 and FUE_(—)31 have a predicted invertase activity and therefore can extend the stay-green characteristics of the plant and therefore increase the overall capacity to store nitrogen in plants for redistribution during grain filling.

Cytokinin is involved, among other processes, in the inhibition of leaf senescence. FUE_(—)55 is a gene with a striking similarity to tRNA isopentenyltransferase, an important enzyme in the cytokinin metabolic pathway. Increased expression of FUE_(—)55 in the roots or shoots will increase the levels of cytokinin leading to enhanced leaf expansion and cell duplication, delayed senescence, increased sink strength of the tissues, enhanced nitrogen utilization, etc.

Zeatin is a naturally occurring cytokinin. FUE_(—)505 is a putative AP2 domain-containing transcription factor that based on microarray experiments it clusters tightly together with ARR genes (Arabidopsis response regulators) which mediate the response of the shoot to cytokinin. ARR genes are Zeatin responsive and are induced after nitrogen addition to nitrogen starved plants. FUE_(—)505 co-regulation together with ARRs indicates a role in the cytokinin response. It is highly likely that constitutive expression of FUE_(—)505 will delay leaf senescence and improve nitrogen utilization and plant growth due to continuous activation of the cytokinin response of the shoot.

Stress Tolerance—

Transgenic plants of the present invention are expected to exhibit tolerance to biotic and abiotic stress.

The phrase “stress” used herein refers to any adverse effect on metabolism, growth, reproduction and/or viability of a plant. Accordingly, abiotic stress can be induced by suboptimal environmental growth conditions such as, for example, salinity, water deprivation, flooding, freezing, low or high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency (including also nutrient inaccessibility such as due to leaching), atmospheric pollution or UV irradiation. Biotic stress can be induced for example by pathogens which are found in the environment.

The phrase “stress tolerance” as used herein refers to the ability of a plant to endure an stress (abiotic) without suffering a substantial alteration in metabolism, growth, productivity and/or viability. Preferably, the genetically engineered plants of the present invention exhibit at least about 2% more, 5% more, 10% more, 20% more, 30% more, 40% more, 50% more, 60% more, 70% more, 80% more, 90% more or even higher tolerance to abiotic stress than non-transgenic plants.

Plants are subject to a range of environmental challenges. Several of these, including salt stress, general osmotic stress, drought stress and freezing stress, have the ability to impact whole plant and cellular water availability. Not surprisingly, then, plant responses to this collection of stresses are related. In a recent review, Zhu notes that “most studies on water stress signaling have focused on salt stress primarily because plant responses to salt and drought are closely related and the mechanisms overlap” (Zhu (2002) Ann. Rev. Plant Biol. 53: 247-273). Many examples of similar responses and pathways to this set of stresses have been documented. For example, the CBF transcription factors have been shown to condition resistance to salt, freezing and drought (Kasuga et al. (1999) Nature Biotech. 17: 287-291). The Arabidopsis rd29B gene is induced in response to both salt and dehydration stress, a process that is mediated largely through an ABA signal transduction process (Uno et al. (2000) Proc. Natl. Acad. Sci. USA 97: 11632-11637), resulting in altered activity of transcription factors that bind to an upstream element within the rd29B promoter. In Mesembryanthemum crystallinum (ice plant), Patharker and Cushman have shown that a calcium-dependent protein kinase (McCDPK1) is induced by exposure to both drought and salt stresses (Patharker and Cushman (2000) Plant J. 24: 679-691). The stress-induced kinase was also shown to phosphorylate a transcription factor, presumably altering its activity, although transcript levels of the target transcription factor are not altered in response to salt or drought stress. Similarly, Saijo et al. demonstrated that a rice salt/drought-induced calmodulin-dependent protein kinase (OsCDPK7) conferred increased salt and drought tolerance to rice when overexpressed (Saijo et al. (2000) Plant J. 23: 319-327).

Exposure to dehydration invokes similar survival strategies in plants as does freezing stress (see, for example, Yelenosky (1989) Plant Physiol 89: 444-451) and drought stress induces freezing tolerance (see, for example, Siminovitch et al. (1982) Plant Physiol 69: 250-255; and Guy et al. (1992) Planta 188: 265-270). In addition to the induction of cold-acclimation proteins, strategies that allow plants to survive in low water conditions may include, for example, reduced surface area, or surface oil or wax production. In another example increased solute content of the plant prevents evaporation and water loss due to heat, drought, salinity, osmoticum, and the like therefore providing a better plant tolerance to the above stresses.

It will be appreciated that some pathways involved in resistance to one stress (as described above), will also be involved in resistance to other stresses, regulated by the same or homologous genes. Of course, the overall resistance pathways are related, not identical, and therefore not all genes controlling resistance to one stress will control resistance to the other stresses. Nonetheless, if a gene conditions resistance to one of these stresses, it would be apparent to one skilled in the art to test for resistance to these related stresses. Methods of assessing stress resistance are further provided in the Examples section which follows.

The ability of the transgenic plants of the present invention to endure stress is expected to affect plant biomass, vigor and yield. The opposite is also anticipated to present good results, essentially, improved biomass, vigor and/or yield is expected to improve the endurance of transgenic plants of the present invention to stress conditions.

As used herein the phrase “plant biomass” refers to the amount or quantity of tissue produced from the plant in a growing season, which could also determine or affect the plant yield or the yield per growing area.

As used herein the phrase “plant vigor” refers to the amount or quantity of tissue produced from the plant in a given time. Hence increase vigor could determine or affect the plant yield or the yield per growing time or growing area.

As used herein the phrase “plant yield” refers to the amount or quantity of tissue produced and harvested as the plant produced product. Hence increase yield could affect the economic benefit one can obtain from the plant in a certain growing time.

To analyze the effect of the transgene on plant physiology, one can assess overall yield and biomass, the tolerance of the plants to fertilizer deficiency and to abiotic stresses such as drought, salinity, cold and heat stresses, freezing, etc. Also of great importance is to assess whether the plant at any of its parts contains an increased content of protein, free amino acids, oil and any other metabolic compounds of value.

The following summarizes assays which may be used to qualify transgenic plants or transgenes of the present invention (further description of these and other assays are provided in the Examples section which follows).

Fertilizer Use Efficiency—

To analyze whether the transgenic plants are more responsive to fertilizers, plants are grown in agar plates or pots with a limited amount of fertilizer. The plants are analyzed for their overall size, time to flowering, yield, protein content of shoot and/or grain. An example methodology of a test for fertilizer use efficiency is provided in the work by Yanagisawa et al (Proc Natl Acad Sci USA. 2004; 101:7833-8) in which seeds of transgenic Arabidopsis are checked for growth rates under limiting-nitrogen conditions (for example at 0.01 mM, 0.05 mM 0.15 mM, 0.3 mM, 1 mM, 3 mM Nitrogen in the form of nitrate or ammonium). The parameters checked are the overall size of the mature plant, its wet and dry weight, the weight of the seeds yielded, the average seed size and the number of seeds produced per plant. Other parameters that may be tested are: the chlorophyll content of leaves (as nitrogen plant status and the degree of leaf verdure is highly correlated), amino acid and the total protein content of the seeds or other plant parts such as leaves or shoots, oil content, etc. Similarly, instead of providing nitrogen at limiting amounts, Phosphate or Potassium can be added at increasing concentrations. Again, the same parameters measured are the same as listed above. In this way, besides Nitrogen Use Efficiency (NUE), Phosphate Use Efficiency (PUE) and Potassium Use Efficiency (KUE) are assessed checking the ability of the transgenic plants to thrive under nutrient restraining conditions.

Nitrogen Determination—

The procedure for N concentration determination in the structural parts of the plants involves the potassium persulfate digestion method to convert organic N to NO₃ ⁻ (Purcell and King 1996 Argon. J. 88:111-113, the modified Cd⁻ mediated reduction of NO₃ ⁻ to NO₂ ⁻ (Vodovotz 1996 Biotechniques 20:390-394) and the measurement of nitrite by the Griess assay (Vodovotz 1996, supra). The absorbance values are measured at 550 nm against a standard curve of NaNO₂. The procedure is described in details in Samonte et al. 2006 Agron. J. 98:168-176.

Grain Protein Concentration—

Grain protein content (g grain protein m⁻²) is estimated as the product of the mass of grain N (g grain N m⁻²) multiplied by the N/protein conversion ratio of k-5.13 (Mosse 1990, supra). The grain protein concentration is estimated as the ratio of grain protein content per unit mass of the grain (g grain protein kg⁻¹ grain).

Oil Content—

The amount of oil expressed as percentage of dry weight. Oil content is defined as the maximum amount of material (lipid) that can be removed from the seed by extraction with specific solvents (usually hexane or petroleum ether). Oil content is measured directly by grinding the seed and extracting the oil in a continuous extractor. Indirect oil content analysis can be carried out using either Nuclear Magnetic Resonance (NMR) Spectroscopy or Near Infrared (NI) Spectroscopy. The NMR technique measures the resonance energy absorbed by hydrogen atoms in the liquid state of the sample while NI utilizes the absorption of near infrared energy (1100-2500 nm) by the sample. While the precision of NIR methods is not as good as extraction methods, NMR methods give very accurate and precise results when calibrated carefully.

Drought Tolerance Assay/Osmoticum Assay—

Tolerance to drought is performed to identify the genes conferring better plant survival after acute water deprivation. To analyze whether the transgenic plants are more tolerant to drought, an osmotic stress produced by the non-ionic osmolyte sorbitol in the medium can be performed. Control and transgenic plants are germinated and grown in plant-agar plates for 4 days, after which they are transferred to plates containing 500 mM sorbitol. The treatment causes growth retardation, then both control and transgenic plants are compared, by measuring plant weight (wet and dry), yield, and by growth rates measured as time to flowering.

Conversely, soil-based drought screens are performed with plants overexpressing the candidate genes detailed above. Seeds from control Arabidopsis plants, or other transgenic plants overexpressing or silencing a polypeptide of the invention are germinated and transferred to pots. Drought stress is obtained after irrigation is ceased accompanied by placing the pots on absorbent paper to enhance the soil-drying rate. Transgenic and control plants are compared to each other when the majority of the control plants develop severe wilting. Plants were re-watered after obtaining a significant fraction of the control plants displaying a severe wilting. Plants are ranked comparing to controls for each of two criteria: tolerance to the drought conditions and recovery (survival) following re-watering.

Salinity Tolerance Assay—

transgenic plants with tolerance to high salt are expected to exhibit better germination, seedling vigor or growth in high salt. Plants differ in their tolerance to NaCl depending on their stage of development, therefore seed germination, seedling vigor, and plant growth responses are evaluated. A salinity tolerance test is taking plants at different developmental stages and irrigate them with increasing concentrations of NaCl (for example 50 mM, 100 mM, 200 mM, 400 mM) applied from the bottom and from above to ensure even dispersal of salt. Transgenic plants are compared to control plants in their external phenotypic appearance, degree of wilting, and overall success to reach maturity and yield progeny at concentrations inhibitory to control plants. Quantitative parameters of tolerance measured are, the average wet and dry weight, and the weight of the seeds yielded, the average seed size and the number of seeds produced per plant. Osmotic stress assays (including NaCl and mannitol assays) are conducted to determine if an osmotic stress phenotype was NaCl-specific or if it was a general osmotic stress related phenotype. Plants tolerant to osmotic stress could also have more tolerance to drought and/or freezing. For salt and osmotic stress germination experiments, the medium is supplemented for example with 50 mM, 100 mM, 200 mM NaCl or 100 mM, 200 mM NaCl, 400 mM mannitol.

Cold Stress Tolerance—

To analyze cold stress, mature (25 day old) plants are transferred to 4° C. chambers for 1 or 2 weeks, with constitutive light. Later on plants are moved back to greenhouse. Two weeks later damages from chilling period, resulting in growth retardation and other phenotypes, are compared between both control and transgenic plants, by measuring plant weight (wet and dry), and by comparing growth rates measured as time to flowering, plant size, yield, etc.

Heat Stress Tolerance—

heat stress tolerance is achieved by exposing the plants to temperatures above 34° C. for a certain period. Plant tolerance is examined after transferring the plants back to 22° C. for recovery and evaluation after 5 days relative to internal controls (non-transgenic plants) or plants not exposed to neither cold or heat stress.

Germination tests compare the percentage of seeds from transgenic plants that could complete the germination process to the percentage of seeds from control plants that are treated in the same manner. Normal conditions are considered for example, incubations at 22° C. under 22-hour light 2-hour dark daily cycles. Evaluation of germination and seedling vigor is conducted between 4 and 14 days after planting. The basal media is 50% Murashige-Skoog medium (MS)+vitamins.

Germination is checked also at unfavorable conditions such as cold (incubating at temperatures lower than 10° C. instead of 22° C.) or using seed imbibition solutions that contain high concentrations of an osmolyte such as sorbitol (at concentrations of 50 mM, 100 mM, 200 mM, 300 mM, 500 mM, and up to 1000 mM) or applying increasing concentrations of salt (of 50 mM, 100 mM, 200 mM, 300 mM, 500 mM NaCl).

Methods of assaying plant vigor, yield and biomass are well known in the art (see Example 9 and Example 10).

The present invention is also valuable for breeding and ornamental purposes. It is thus envisaged that polynucleotides and polypeptide sequences of the present invention which are associated with root architecture (FUE_(—)34_Evo, SEQ ID NO: 54, see also Example 11 and FIG. 8) may also be used to govern plant tillering and as such may be upregulated or downregulated to govern branching and tillering. Methods of downregulating gene expression in plants are well known in the art.

Thus, the present invention is of high agricultural value for promoting commercially desired traits in crop-plants.

As used herein the term “about” refers to ±10%.

Additional objects, advantages, and novel features of the present invention will become apparent to one ordinarily skilled in the art upon examination of the following examples, which are not intended to be limiting. Additionally, each of the various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below finds experimental support in the following examples.

EXAMPLES

Reference is now made to the following examples, which together with the above descriptions, illustrate the invention in a non limiting fashion.

Generally, the nomenclature used herein and the laboratory procedures utilized in the present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the literature. See, for example, “Molecular Cloning: A laboratory Manual” Sambrook et al., (1989); “Current Protocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., “Current Protocols in Molecular Biology”, John Wiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide to Molecular Cloning”, John Wiley & Sons, New York (1988); Watson et al., “Recombinant DNA”, Scientific American Books, New York; Birren et al. (eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, Cold Spring Harbor Laboratory Press, New York (1998); methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis, J. E., ed. (1994); “Current Protocols in Immunology” Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds), “Basic and Clinical Immunology” (8th Edition), Appleton & Lange, Norwalk, Conn. (1994); Mishell and Shiigi (eds), “Selected Methods in Cellular Immunology”, W. H. Freeman and Co., New York (1980); available immunoassays are extensively described in the patent and scientific literature, see, for example, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521; “Oligonucleotide Synthesis” Gait, M. J., ed. (1984); “Nucleic Acid Hybridization” Hames, B. D., and Higgins S. J., eds. (1985); “Transcription and Translation” Hames, B. D., and Higgins S. J., Eds. (1984); “Animal Cell Culture” Freshney, R. I., ed. (1986); “Immobilized Cells and Enzymes” IRL Press, (1986); “A Practical Guide to Molecular Cloning” Perbal, B., (1984) and “Methods in Enzymology” Vol. 1-317, Academic Press; “PCR Protocols: A Guide To Methods And Applications”, Academic Press, San Diego, Calif. (1990); Marshak et al., “Strategies for Protein Purification and Characterization—A Laboratory Course Manual” CSHL Press (1996); all of which are incorporated by reference as if fully set forth herein. Other general references are provided throughout this document. The procedures therein are believed to be well known in the art and are provided for the convenience of the reader. All the information contained therein is incorporated herein by reference.

Example 1 Polynucleotide Identification and Gene Role Prediction Using Bioinformatics and Molecular Tools

Polynucleotides, suitable for increasing FUE and/or abiotic or biotic stress tolerance were identified by in-depth analysis of RNA expression profiles, sequence similarities, gene annotations, biochemical pathways, DNA, ESTs, protein and expression databases, which are publicly available and used as input data to a series of proprietary computational algorithms that allow expert data mining.

Trait association was performed using accurate expression profiling by means of quantitative Real Time PCR, to correlate between the expression levels in different tissues and under specific growth conditions for elucidating the function of the expressed polynucleotide.

Materials and Methods

Identifying Polynucleotide Sequences Associated with Increased FUE

The present methodology is based on three stages described in the following examples, essentially the bioinformatic filtering, molecular analysis and in planta validation. Infra is a description of the bioinformatic algorithm.

A. Bioinformatic Filtering:

Clustering DNA Sequences into Gene Clusters—

The aim of EST (Expressed Sequence Tag) clustering is to incorporate all ESTs that share a transcript or gene parent to the same cluster. Typically, clustered ESTs are assembled into one or more consensus sequences (contigs) that reflect the transcript diversity, providing these contigs such that the information they contain most truly reflects the sampled biology. A gene cluster is fragmented, EST data and (if known) gene mRNA sequence data, consolidated, placed in correct context and indexed by gene such that all expressed data concerning a single gene is in a single index class, and each index class contains the information for only one gene (Burke et al, 1999, D2_cluster: A Validated Method for Clustering EST and Full-length cDNA Sequences. Genome Research, 9(11), 1135-1142). The Compugen LEADS™ platform (Hypertext Transfer Protocol://World Wide Web (dot) cgen (dot) com/research/Publications/LEADSwhitepaper.pdf) was used for the assembly.

Calculating the Digital Expression for all the Gene Clusters in Several Plant Species—

Digital expression, also known as electronic northern blot, compares occurrences of large number of random ESTs from non-normalized cDNA libraries. The variation in the relative frequency of those tags, stored in databases, is then used to elucidate the differential expression of the corresponding genes. Digital Northern data can be used to provide quantitative assessment of differential expression between different organs in the plant or at different physiological states (stress versus normal). This tool displays virtual expression profiles of genes based on the EST sequences forming the cluster. The tool can provide the expression profile of a cluster in terms of plant anatomy (i.e., in what tissues/organs is the gene expressed), developmental stage (i.e., the developmental stages at which a gene can be found) and profile of treatment (i.e., provides the physiological conditions under which a gene is expressed such as drought, cold, pathogen infection and the like). Given a random distribution of ESTs in the different clusters, the digital expression provides a probability value that describes the probability of a cluster having a total of N ESTs to contain X ESTs from a certain collection of libraries. For the probability calculations the following is taken into consideration: a) the number of ESTs in the cluster, b) the number of ESTs originating from a specific library or a group of related libraries, c) the overall number of ESTs available representing the species. In this way clusters with low probability values are highly enriched with ESTs from the group of libraries of interest indicating a specialized expression. In addition, a proprietary vocabulary (limited compendium of terms) is used that takes into consideration the annotation of each EST library and uses specific keywords to describe the experimental data associated with the sequences with regards to tissue type, treatment and developmental stages. The terms chosen from the proprietary vocabulary are combined with the calculated digital expression to build an expression profile for each specific gene, based on the source of the libraries that provide the sequences to the gene cluster. A statistic and graphic representation of this profile is built for the digital expression calculations. Because the annotations are from a controlled vocabulary, the entire database is dissected with specific keywords describing specific tissues, developmental stages or treatments.

Integrating all Relevant Data for Each Gene, Including Expression Data from Microarray Experiments, Digital Expression, Annotation, Ontology, Gene Families, Conserved Motifs and the Like—

A proprietary tool that creates groups of orthologous genes from genomic databases from multiple plant species is used. In order to provide further support to the genes identified, orthologous genes or the orthologous group is tested as a whole to see involvement of the trait of interest according to the keywords that are most significant in their calculated digital expression.

Gene Selection—

This is done according to several biologically sound assumptions to query the database described above. Gene selection is done by filtering specific groups of genes using carefully selected criteria. The final set of genes should contain a limited number of genes, which one could handle in the following molecular analysis and transgenic experiments. The different criteria utilized herein are described with great detail for each gene below.

Gene selection for this invention takes into consideration several concepts widely accepted in plant science. Nutrient deficiencies cause adaptations of the root architecture, particularly notably for example is the root proliferation within nutrient rich patches to increase nutrient uptake. Nutrient deficiencies cause also the activation of plant metabolic pathways which maximize the absorption and assimilation processes. In this process, genes are triggered and activated causing the architectural change (Jose Lopez-Bucio et al, The role of nutrient availability in regulating root architecture, Current Opinion in Plant Biology 2003, 6:280-287). Engineering the expression of the triggered genes may cause the plant to exhibit the architectural changes and enhanced metabolism also under other conditions. Second, it is widely known that the plants usually respond to drought by creating a deeper root system that allows access to moisture located in deeper soil layers (Morgan, J. M., and A. G. Condon. 1986. Water use, grain yield, and osmoregulation in wheat. Aust. J. Plant Physiol. 13:523-532 and Yiwei Jiang and Bingru Huang, 2001, Crop Science 41:1168-1173). Triggering this effect will allow the plants to access nutrients located in deeper soil horizons particularly those readily dissolved in water like nitrates. Third, different abiotic stresses (e.g., drought, osmoticum, cold, heat, radiation, salinity, nutrient deficiencies, and the like) elicit their response using both: stress-specific as well as common stress pathways (Gabriela M. Pastori and Christine H. Foyer, Common Components, Networks, and Pathways of Cross-Tolerance to Stress, Plant Physiol, June 2002, Vol. 129, pp. 460-468). This provides the possibility to distinguish between the genes that are involved in each pathway.

The plant response to stress is costly in terms of energy as such affecting plant yield. Precise engineering of specific genes provides the ability to activate only partially a stress response without causing the concomitant loss in yield. Accordingly, several queries to distinguish the genes that are activated during the common and stress-specific responses were performed. Since some of the plant responses such as enhanced root system or superior storage capabilities are highly preferred also at optimal growing conditions, the present invention envisages to create modified plants with improved FUE that show in addition also enhanced response to other abiotic plant stresses that cause adverse effects on yield.

For the purpose of the identification FUE improving genes, 416899 EST and 23563 mRNA transcript sequences from Maize were extracted from Genbank release 145 (December 2004), cleaned by screening for vectors, low-complexity sequences and known repeats from public databases, and then clustered and assembled into contigs using Compugen's LEADS platform.

The EST libraries in Genbank 146 for Maize and other species such as Soybean, Tomato, Barley, Sorghum, Rice, Cotton, Wheat and Arabidopsis were examined and annotated using keywords describing the plant tissue used, the treatment applied to grow the plants and the developmental stage of the plants when the tissues were taken. A significance value was assigned to the frequency of ESTs in each contig from each EST library or set of libraries sharing the same annotation. The significance value was based on a statistical test that takes into account the number of ESTs from the given category in the contig, the number of these ESTs in the whole production, the size of the contig and the total number of ESTs in the production.

In addition Arabidopsis microarray experiments, freely available at the Nottingham Arabidopsis Stock Centre (NASC, Hypertext Transfer Protocol://affymetrix (dot) arabidopsis (dot) info/) comprising experiments describing anatomy, development and various stress experiments were integrated. To link the contigs of the LEADS Maize production to the corresponding cluster from other species orthologue finder algorithm was employed that uses among other filters, reciprocal BLAST analysis to identify the most similar gene in other plant species.

The following describes the parameters which were used for selecting each gene. Table 1 below associates internal identifiers (NUE_XXX or FUE_XXX which are interchangeably used) to SEQ ID Nos.

TABLE 1 Internal SEQ ID NO: SEQ ID NO: Identifier (polynucleotide) (polypeptide) Plant FUE 1 1 110 maize 2 111 rice 3 112 soybean FUE 2 41318 113 maize FUE 3 5 114 maize 6 115 barley 7 116 rice FUE 4 8 117 maize FUE 5 9 118 maize 10 119 rice FUE 40 11 120 maize (6/40) 12 121 sorghum FUE 7 131323 122 maize 14 123 sorghum 15 124 barley FUE 8 161324 125 maize 17 126 sorghum 18 127 rice FUE 9 191325 128 maize FUE 10 20 129 maize 21 130 soybean 1 22 131 soybean 2 FUE 11 23 132 maize FUE 12 241327 133 maize 25 134 barley 26 135 sorghum FUE 13 27 136 maize 28 137 barley 29 138 rice FUE 14 301329 139 maize 31 140 barley FUE 15 32 141 maize 33 142 barley 34 143 rice 35 144 tomato 36 145 soybean 1 FUE 16 37 146 maize 38 147 barley 39 148 rice 40 149 soybean 41 150 tomato FUE 17 42 151 maize 43 152 barley 44 153 sorghum 45 154 rice 46 155 soybean 1 47 156 soybean 2 48 157 tomato FUE_30 49 158 maize FUE_31 50 159 maize FUE_32 51389 160 maize 52 161 wheat FUE_33 53 162 maize FUE_34_evo 54 163 maize FUE_34_Pat 55 164 maize FUE_35 56 165 maize FUE_36 57 166 maize FUE_37 58 167 maize 59 168 barley 60 169 wheat 61 170 sugarcane 62 171 rice 63 172 soybean FUE_38 64 173 maize 65 174 barley 66 175 sorghum 67 176 soybean FUE_39 68 177 maize FUE_41 69 178 maize FUE_43 70 1791186 maize 71 180 rice 72 181 sorghum FUE_44 73 182 maize 74 183 soybean 75 184 barley 76 185 sorghum FUE_45 77 186 maize FUE_46 78673 1871222 maize FUE_47 79 188 maize FUE_48 80 189 maize 81 190 rice 82 191 barley 83 192 sorghum FUE_49 841335 1931243? maize 85 194 sorghum FUE_50 86699 1951248 maize FUE_51 87 196 maize 88 197 sorghum 89 198 barley 90 199 barley 2 91 200 wheat 1 92 201 wheat 2 FUE_52 93 202 maize FUE_53 94 203 maize 95 204 sorghum 96 205 rice 97 206 wheat FUE_54 98 207 maize 99 208 sorghum 100 209 rice FUE_55 101739 2101288 maize FUE_100 102 211 maize FUE_101 103 212 maize FUE_102 104 213 maize FUE_501 105 214 Arabidopsis thaliana FUE_502 106 215 Arabidopsis thaliana FUE_503 107 216 Arabidopsis thaliana FUE_504 108 217 Arabidopsis thaliana FUE_505 109 218 Arabidopsis thaliana

Of note, overexpression Fold (“Fold”) is calculated as the ratio between the number of ESTs found in a gene or an orthologue group for a certain category (“Keyword”) and the number of expected ESTs according to a normal distribution. A probabilistic value (P-value) was estimated for the calculated overexpression folds. Genes were selected based on the results presented here and other computational filtering combined with manual curation as detailed above.

FUE_(—)1 was selected for its strong root expression in maize (as shown in Table 2 and FIGS. 2A and 2B), as well as the expression pattern of its orthologues such as in soybean and rice (as shown in Table 3 and FIGS. 2C and 2D). In addition, FUE_(—)1 displays some homology to RCc3 protein (GENEBANK Accession NO. L27208) a known root specific protein putatively associated with lipid transport.

TABLE 2 Digital expression of FUE_1 in maize: Anatomy Primary Secondary ESTs ESTs Key- Key- in in Pro- Expected word word Gene duction ESTs Fold p-value flower 4 89278 10.8145 0.369873 0.997498 seedling + 4 9012 1.09165 3.66417 0.0234977 female flower leaf 1 35689 4.32312 0.231314 0.989277 ear leaf 1 7960 1 1 0.622546 mix 2 90046 10.9076 0.183359 0.999938 root 37 36059 4.36794 8.47082 1.78E−15 primary 24 33886 4.10472 5.84693 7.82E−14 root system root tip 13 2173 1 13 2.22E−15 seedling 6 32466 3.93271 1.52567 0.19702 seedling + 4 9012 1.09165 3.66417 0.0234977 female flower shoot 1 16152 1.95654 0.511106 0.864469

TABLE 3 Digital expression of FUE_1 ortholog group: Anatomy cell germinating callus cambium suspension flower seed leaf mix phloem pod root seedling cotton 0.26 grape 0.39 maize 0.07 0.06 0.4 2.61 0.2 poplar 2.8 4.1 rice 0.9 0.08 5.25 1.24 sorghum 0.46 2 0.21 soybean 1 0.31 0.11 tomato 1.46 TOTAL 1.92 2.8 2 0.47 0.9 0.14 0.4 4.1 1 8.17 2.02

FUE_(—)2 is a protein of unknown function displaying a digital expression linking it to roots and particularly to roots under drought stress.

FUE_(—)3 is a putative non-specific lipid transfer protein expressed particularly in roots in maize (Table 4 and Table 5), but also in barley and rice. Its expression in roots under drought is conserved throughout evolution in sorghum, maize, rice and barley (as shown in Table 6 and 7). There are indications that the gene is expressed also under salinity stress in barley and rice and under nitrogen deficiency in barley.

TABLE 4 Digital expression of FUE_3 in maize: Anatomy Secondary ESTs in ESTs in Keyword Keyword Gene Production Expected ESTs Fold p-value flower 1 89278 7.82327 0.127824 0.999862 seedling + 1 9012 1 1 0.550246 female flower mix 2 90046 7.89057 0.253467 0.998578 root 30 36059 3.15978 9.49432 2.66E−15 primary root 30 33886 2.96937 10.1032 0 system seedling 2 32466 2.84494 0.703003 0.789648 seedling + 1 9012 1 1 0.550246 female flower shoot 1 16152 1.41537 0.706529 0.764428

TABLE 5 Digital expression of FUE_3 in maize: Treatment Secondary ESTs in ESTs in Keyword Keyword Gene Production Expected ESTs Fold p-value drought 30 21216 1.85912 16.1367 3.44E−15 water stress 17 6113 1 17 0 48 h water stress 6 6417 1 6 1.84E−05 5 h water stress 7 2720 1 7 3.76E−09 5 h and 48 h, Subtracted library mix 2 36475 3.19624 0.625736 0.8422

TABLE 6 Digital expression of FUE_3 ortholog group: Anatomy germinating culm flower seed grain leaf mix rachis root seedling shoot barley 1 0.39 0.19 0.03 2.24 1.4 0.18 maize 0.07 0.34 2.66 0.08 rice 0.24 0.9 0.31 0.2 sorghum 0.67 TOTAL 1 0.07 0.39 0.19 0.95 0.34 2.24 4.95 0.58 0.2

TABLE 7 Digital expression of FUE_3 ortholog group: Treatment light nutrient photoperiod drought response mix deficiencies pathogen response salinity waterlogged barley 0.81 0.92 0.53 0.07 1 maize 6.51 0.83 rice 2.29 8 3.48 sorghum 1.61 0.34 TOTAL 11.22 0.92 0.83 0.53 0.42 8 3.48 1

FUE_(—)4 is also a protein of unknown function displaying specific digital expression under drought stress (as shown in Table 8 and 9).

TABLE 8 Digital expression of FUE_4 in maize: Anatomy Key- Secondary ESTs in ESTs in Expected word Keyword Gene Production ESTs Fold p-value root 6 36059 1 6 6.44E−07 primary root 6 33886 1 6 4.44E−07 system

TABLE 9 Digital expression of FUE_4 in maize: Treatment ESTs in ESTs in Expected Keyword Gene Production ESTs Fold p-value drought 6 21216 1 6 2.67E−08 water 3 6113 1 3 7.54E−05 stress 48 h water 3 6417 1 3 8.71E−05 stress 5 h

to FUE_(—)5 is a Ubiquinol-cytochrome C reductase complex like protein expressed under several stresses and particularly under drought and salinity in maize (as shown in Table 10) and rice roots.

TABLE 10 Digital expression of FUE_5 in maize: Treatment Secondary ESTs in ESTs in Expected Keyword Keyword Gene Production ESTs Fold p-value drought 16 21216 2.67932 5.97167 3.75E−09 CONTROL 1 5966 1 1 0.532021 well watered 0 h water stress 9 6113 1 9 6.92E−08 48 h water stress 4 6417 1 4 0.00876739 5 h water stress 2 2720 1 2 0.0465022 5 h and 48 h, Subtracted library mix 3 36475 4.60634 0.651276 0.851418 pathogen 1 2260 1 1 0.248934 Fusarium, 6 h 1 667 1 1 0.0808552 post infection salinity 3 3579 1 3 0.0105368 150 mM 3 3579 1 3 0.0105368 NaCl 24 h

FUE_(—)6 displays homology to a multiple stress-associated zinc-finger protein, expressed in maize during grain development and in roots, particularly under drought stress (as shown in Tables 11 and 12 respectively). The present inventors uncovered that FUE_(—)6 and FUE_(—)40 are part of the same transcript. FUE_(—)6 represents the 5′ region of the transcript, while FUE_(—)40 the 3′ region. For convenience, this transcript is presented in this herein under the name FUE_(—)40.

TABLE 11 Digital expression of FUE_6 in maize: Anatomy ESTs Key- Secondary in ESTs in Expected word Keyword Gene Production ESTs Fold p-value grain 1 73038 2.07065 0.48294 0.899148 glume 1 2043 1 1 0.0564193 root 10 36059 1.02228 9.78202 4.83E−10 primary 10 33886 1 10 2.61E−10 root system

TABLE 12 Digital expression of FUE_6 in maize: Treatment ESTs Key- Secondary in ESTs in Expected word Keyword Gene Production ESTs Fold p-value drought 10 21216 1 10 2.50E−12 CONTROL 2 5966 1 2 0.011856 well watered 0 h water stress 1 6113 1 1 0.16028 48 h water stress 4 6417 1 4 2.25E−05 5 h water stress 3 2720 1 3 5.44E−05 5 h and 48 h, Subtracted library

FUE_(—)7 is a hypothetical protein displaying similarity to antifreeze protein expressed predominantly in barley and maize in roots and with a more evident expression during drought stress (as shown in Table 13 and 14).

TABLE 13 Digital expression of FUE_7 ortholog group: Anatomy flower grain leaf mix root seedling barley 0.96 0.33 1.86 0.21 maize 0.15 0.83 0.39 4.28 0.34 sorghum 1.13 TOTAL 0.15 1.79 1.46 0.39 6.14 0.55

TABLE 14 Digital expression of FUE_7 ortholog group: Treatment drought pathogen salinity waterlogged barley 3.47 0.38 1 maize 9.64 1 sorghum 7.75 TOTAL 20.87 0.38 1 1

to FUE_(—)8 displays homology to Acyl-ACP thioesterase and expressed in maize roots under drought stress (as shown in Table 15). The sorghum and rice orthologues show also a clear association to drought as revealed by the source of the sequences composing the genes.

TABLE 15 Digital expression of FUE_8 in maize: Anatomy ESTs Secondary in ESTs in Expected Keyword Keyword Gene Production ESTs Fold p-value root 6 36059 1 6 6.44E−07 primary 6 33886 1 6 4.44E−07 root system

FUE_(—)9 is a hypothetical protein expressed in maize roots under drought stress.

FUE_(—)10 displays homology to electron transport-associated proteins. displaying a strong root expression solely associated to drought in maize (as shown in Table 16 and 17) and to other abiotic stresses as found for its orthologue expression in soybean.

TABLE 16 Digital expression of FUE_10 in maize: Anatomy Secondary ESTs in ESTs in Keyword Keyword Gene Production Expected ESTs Fold p-value flower 1 89278 3.22135 0.310429 0.974291 seedling + 1 9012 1 1 0.280367 female flower grain 1 73038 2.63537 0.379453 0.946054 pericarp 1 9389 1 1 0.290325 mix 2 90046 3.24906 0.615563 0.870275 root 8 36059 1.30109 6.1487 9.97E−06 primary root 8 33886 1.22268 6.543 6.26E−06 system seedling 2 32466 1.17145 1.70729 0.329608 seedling + 1 9012 1 1 0.280367 female flower shoot 1 16152 1 1 0.448596

TABLE 17 Digital expression of FUE_10 in maize: Treatment ESTs Key- Secondary in ESTs in Expected word Keyword Gene Production ESTs Fold p-value drought 8 21216 1 8 1.78E−07 water 5 6113 1 5 1.72E−06 stress 48 h water 2 6417 1 2 0.0218099 stress 5 h water 1 2720 1 1 0.093796 stress 5 h and 48 h, Subtracted library mix 2 36475 1.3161 1.51964 0.384279

FUE_(—)11 displays homology to the physical impedance induced protein and is expressed in maize in roots also during drought stress.

FUE_(—)12 is an unknown protein expressed in maize roots under water stress (drought) and in other abiotic stresses such as drought in barley and under nitrogen deficiency and heat stress in sorghum.

FUE_(—)13 displays homology to Pathogenesis-related protein 10, and is expressed in different stresses in maize (drought, pathogens as Fusarium). The barley and rice orthologues are strongly expressed particularly under abiotic and biotic stresses linking this protein to the ubiquitous plant response to stress.

FUE_(—)14 is a maize protein displaying homology to Germin-like protein 6. The digital expression of its barley orthologue links this protein to pathogen response, as well as drought and nitrogen deficiency response.

FUE_(—)15 is a putative auxin-regulated protein also expressed in maize roots. Its orthologues from barley, rice and are related to drought as well as other biotic and abiotic stresses such as pathogen response. In tomato and soybean, the protein is linked to the response to pathogens and nutrient deficiencies.

FUE_(—)16 is an Uclacyanin 3-like protein, expressed strongly in maize roots under water stress (as shown in Table 18 and 19). Its orthologues from barley, rice, soybean and tomato are also expressed in roots but involved in the response to other several biotic and abiotic stresses particularly to light response (as shown in Table 20 and 21).

TABLE 18 Digital expression of FUE_16 in maize: Anatomy Secondary ESTs in ESTs in Keyword Keyword Gene Production Expected ESTs Fold p-value flower 3 89278 3.91163 0.766943 0.78613 seedling + 3 9012 1 3 0.00667346 female flower root 14 36059 1.57989 8.86136 1.86E−12 primary root 14 33886 1.48468 9.42961 7.90E−13 system seedling 3 32466 1.42247 2.10901 0.165456 seedling + 3 9012 1 3 0.00667346 female flower

TABLE 19 Digital expression of FUE_16 in maize: Treatment ESTs ESTs in Key- Secondary in Pro- Expected word Keyword Gene duction ESTs Fold p-value drought 14 21216 1 14 3.77E−15 CONTROL 2 5966 1 2 0.0275854 well watered 0 h water stress 4 6113 1 4 0.000124308 48 h water stress 6 6417 1 6 2.16E−07 5 h water stress 2 2720 1 2 0.00622988 5 h and 48 h, Subtracted library

TABLE 20 Digital expression of FUE_16 ortholog group: Anatomy seed- culm flower leaf mix root seed ling shoot xylem barley 1 0.45 0.1  0.48 maize 0.17 2.14 0.48 poplar 0.24 1.57 rice 0.33 3.62 0.51 sorghum 0.4  soybean 0.49 0.04 0.07 0.43 3 0.71 0.46 tomato 0.48 TOTAL 1 1.11 0.14 0.41 7.41 3 2.11 0.46 1.57

TABLE 21 Digital expression of FUE__16 ortholog group: Treatment chemical cold heat light nutrient treatment stress drought stress response nodulation deficiencies pathogen salinity barley 0.63 maize 3.98 poplar 1.12 rice 1 0.63 2 sorghum 1.9 soybean 1 1 1 1.56 5 2.85 1.09 tomato 1.12 TOTAL 2 1 3.98 1 4.73 5 5.09 1.09 2

FUE_(—)17 is a hypothetical protein displaying a digital expression in maize and other plant species linking it to a response to drought (maize, barley and sorghum), to pathogens (rice, soybean and tomato) and to nitrogen deficiency and water-logging in barley.

FUE_(—)30 and FUE_(—)31 were selected because of their annotation and the significant EST content derived from root particularly in the case of FUE_(—)30. FUE_(—)30 and FUE_(—)31 have a predicted invertase activity, an enzyme which is known to delay senescence when expressed under a senescence-activated promoter (Balibrea Lara, et al. Plant Cell 16: 1276-1287, 2004). FUE_(—)30 can extend the stay-green characteristics of the plant and therefore increase the overall capacity to store nitrogen in plants for redistribution during grain filling.

FUE_(—)32 is annotated as major intrinsic like protein and its wheat orthologue contains several sequences isolated from root. In addition, the maize gene selected shows homology to Brevis Radix. Brevis Radix is a novel regulator of cell proliferation and elongation that when inactive it creates plants with shorter roots (Mouchel at al., Genes and Development Vol. 18:700-714, 2004).

FUE_(—)54 displays homology to an Auxin responsive protein. The genes contain a significant EST annotation from roots and stressed tissues, as well as its best orthologue from sorghum and rice that are specially expressed under stress conditions and probably enriched in the root.

FUE_(—)33 and FUE_(—)100 encode for nitrilases. Nitrilase is an important enzyme in the auxin biosynthetic pathway that converts 3-indoleacetonitrile to 3-indole-acetic acid (auxin). Increased expression of Nitrilases in the root will enlarge the overall auxin levels and induce root elongation, secondary root formation, enhanced gravitropic response, etc.

FUE_(—)34 and FUE_(—)35 as well as FUE_(—)46 and FUE_(—)47 are probable transcription factors both expressed particularly in stressed roots as judged by the EST libraries providing the sequences of the genes. As these transcription factors are highly associated with water stressed libraries it may occur that modifying the expression of these genes will activate the genes that induce the structural and metabolic changes associated with stresses.

FUE_(—)36, FUE_(—)37 and FUE_(—)38 show some degree of similarity to ABA-responsive genes and/or stress annotated genes, and have a significant content of sequences derived from root libraries. FUE_(—)36 has probably protein kinase activity with a striking similarity to a SAPK8, a protein that its expression levels are increased during ABA treatment or under salinity conditions, demonstrating a role in the stress response. FUE_(—)37 has almost all the sequences derived from root and particularly root under water stress (as shown in Tables 22 and 23). The orthologues from barley, wheat and sugar cane also support the contention that the gene is mainly expressed in roots. There are indications that this gene is implicated in the response to water stress deprivation, hyperosmotic salinity response, cold and other stresses.

TABLE 22 Digital expression of FUE_37 ortholog group: Anatomy seed- callus fruit leaf mix root ling stem xylem barley 0.35 0.84 0.24 grape 2.37 maize 0.26 0.84 poplar 0.09 7 rice 0.26 0.34 soybean 0.29 0.2  0.31 0.21 1 TOTAL 0.55 2.37 0.99 0.57 1.9  0.24 1 7

TABLE 23 Digital expression of FUE_37 ortholog group: Treatment hormone drought treatment mix nodulation pathogen salinity barley 1.19 0.14 maize 0.4 1 rice 2.38 0.36 soybean 0.4 0.69 1 TOTAL 4.37 0.36 0.69 1 0.14 1

FUE_(—)38 is derived from various stressed root libraries (as shown in Tables 24 and 25) and displays a notorious similarity to PKABA1. PKABA1 transcript levels are barely detectable in growing seedlings but are induced dramatically when plants are subjected to dehydration, cold and osmotic stress (Holappa L D and Walker-Simmons M K Plant Physiol. Vol. 108:1203-1210, 1995). A modified expression pattern for this gene can provide increased abiotic stress tolerance, increased vigor, increased yield and better use efficiency of fertilizers.

TABLE 24 Digital expression of FUE_38 ortholog group: Anatomy Secondary ESTs in ESTs in Expected Keyword Keyword Gene Production ESTs Fold p-value cell culture 3 16132 1 3 0.0367348 flower 1 89278 4.14173 0.241445 0.990968 seedling + 1 9012 1 1 0.344935 female flower grain 1 73038 3.38834 0.29513 0.976577 endosperm 1 25774 1.19569 0.836336 0.709829 mix 2 90046 4.17736 0.478771 0.944464 root primary root 10 33886 1.57202 6.36125 5.83E−07 system seedling 1 32466 1.50614 0.663948 0.792566 seedling + 1 9012 1 1 0.344935 female flower

TABLE 25 Digital expression of FUE_38 ortholog group: Treatment hormone light mechanical drought treatment response treatment mix nodulation pathogen salinity barley 0.26 0.93 maize 2.3 0.45 0.93 rice 0.65 0.13 sorghum 0.26 0.46 2 0.93 soybean 0.26 2.75 0.14 TOTAL 3.07 0.46 0.65 2 0.45 2.75 0.27 2.8

FUE_(—)48 was selected using microarray Arabidopsis expression data available at (Hypertext Transfer Protocol://affymetrix (dot) arabidopsis (dot) info/narrays/supersearch (dot) pl?searchterms=afgn). Genes with enriched expression in roots and highly responsive to ABA and abiotic stresses (salinity, osmoticum and cold) were identified. One of the genes had an orthologue in maize (FUE_(—)48) that showed enhanced content of root-derived sequences. The probable sorghum orthologue is a gene mainly composed by stress-derived sequences, particularly from water stress and drought conditions (as shown in Table 26). FUE_(—)48 shows similarity to SIP (Seed Imbibition Protein).

TABLE 26 Digital expression of FUE_48 ortholog group: Treatment heat hormone light nutrient drought stress treatment response nematode deficiencies pathogen salinity barley 0.98 cotton 0.09 maize 0.73 0.18 poplar 0.11 0.23 0.25 rice 0.51 0.19 0.27 0.53 sorghum 3.20 0.71 0.04 0.15 soybean 0.41 1.78 0.40 0.16 0.18 tomato 0.12 0.13 TOTAL 5.42 0.71 0.27 0.75 1.78 0.76 0.77 0.89

FUE_(—)39 is a root-expressed calcineurin B-like Ca⁺⁺ binding protein. Calcineurins are Ca⁺⁺ sensing protein kinases differentially regulated by stress conditions such as salt, drought, cold, and wounding stress. Calcium is involved in several root important behaviors such as gravitropism, hydrotropism, etc and is an important second messenger for various signal transduction pathways. Continuous activation of the protein cascade in which FUE_(—)39 is involved can provide advantageous properties or desired traits compared to a reference plant, including improved abiotic stress tolerance, increased vigor and yield, improved use of fertilizer, etc.

FUE_(—)40 and FUE_(—)41 are genes expressed in roots particularly at stress conditions. The sorghum orthologue of FUE_(—)40 has several sequences derived from stressed tissues including roots. FUE_(—)41 and FUE_(—)40 show similarity to stress-responsive proteins. FUE_(—)43, FUE_(—)44 and FUE_(—)45 have a distant similarity to an E. coli universal stress protein and their composing sequences contain a significant fraction of root stressed tissues (as shown in Table 27 for FUE_(—)43 and in Table 28 for FUE_(—)44). FUE_(—)43 shows similarity to an ethylene-responsive protein. FUE_(—)44 and FUE_(—)45 show a weak similarity to an early nodulin-like protein. Those proteins expressed ectopically under a different promoter are likely to produce favorable effects in the transgenic plants such as enhanced stress tolerance, improved growth at optimal and adverse conditions mainly due to probable modifications in the root architecture.

TABLE 27 Digital expression of FUE_43 ortholog group: Treatment Control hormone light nutrient Library drought treatment response mix nodulation deficiencies pathogen salinity barley 1.00 0.33 0.09 maize 1.42 1.55 0.83 rice 0.83 1.64 sorghum 1.60 0.91 0.63 soybean 0.43 0.81 0.22 tomato 0.10 TOTAL 1.00 3.86 0.43 2.88 1.55 0.81 0.63 0.41 0.83

TABLE 28 Digital expression of FUE_44 ortholog group: Treatment chemical light nutrient treatment drought response nematode deficiencies pathogen salinity waterlogged barley 0.66 0.28 grape 0.07 maize 0.92 1.69 poplar 0.52 0.20 rice 0.50 0.07 sorghum 0.66 0.50 soybean 3.00 0.44 0.33 2.00 1.30 0.08 0.85 5.00 tomato TOTAL 3.00 2.67 1.34 2.00 1.82 0.69 2.54 5.00

FUE_(—)50 was selected using microarray Arabidopsis expression data in which root specific genes were selected if they were also auxin and ethylene responsive. According to the calculated digital expression, the maize orthologue presented in this invention is expressed in roots under water stress conditions and in pathogenesis related tissues. The maize gene shows similarity to nodulin, a protein known to be involved during nodule and lateral root development (Papadopoulou et al. Plant Mol Biol. 1996; 30:403-17).

FUE_(—)501 is a putative Arabidopsis thaliana amino acid transporter that shows increased expression under salinity, osmoticum and is also Abscisic acid responsive (ABA—abiotic stress response hormone). FUE_(—)51, a maize homologue of FUE_(—)501 is composed mainly by sequences derived from stressed root sequences and has a tentative annotation as an amino acid transporter. The sorghum orthologue of FUE_(—)51 is involved in stress responses according to the digital expression. Its barley orthologue has sequences derived from roots and stressed roots. Also the wheat orthologue shows several sequences derived from root.

FUE_(—)502 is a putative amino acid transporter which shows increased expression during salinity stress and osmoticum both in roots and shoots. FUE_(—)52, its closest maize orthologue, has also similarity to amino acid transport proteins and has a significant representation of root and stressed root derived sequences.

FUE_(—)503 has an impressive expression in seeds suggesting a strong role in uptake of amino acids into the developing seeds. In addition the gene is strongly upregulated under salinity and in response to methyl jasmonate. FUE_(—)504 was chosen because of its strong response to ABA, to salinity (specially of the shoot), to osmoticum, and cold. FUE_(—)49 shows a strong similarity at the level of translated amino acids to FUE_(—)504 but low at the level of coding nucleotides. Its sorghum orthologue has sequences significantly derived from water stress/drought libraries.

FUE_(—)53 is a putative amino acid transporter with almost of all the sequences composing the genes derived from root and particularly stressed roots. The sorghum, rice and wheat orthologues contain several sequences derived from root and root under stress libraries.

FUE_(—)101 and FUE_(—)102 show similarity to amino acid transporters. FUE_(—)102 is specifically composed from sequences derived from cold treated seedlings and pathogen infected corn ear tip.

FUE_(—)55 is a gene with a striking similarity to tRNA isopentenyltransferase, an important enzyme in the cytokinin metabolic pathway. Increased expression of FUE_(—)55 in the roots or shoots will increase the levels of cytokinin leading to enhanced leaf expansion and cell duplication, delayed senescence, increased sink strength of the tissues, enhanced nitrogen utilization, etc. FUE_(—)55 is particularly expressed in the endosperm, a tissue that is probably the strongest sink in the plant.

FUE_(—)505 is a putative AP2 domain-containing transcription factor present in two important list of genes. One list contains the genes that are Zeatin responsive (Zeatin is a naturally occurring cytokinin) while the second list of genes contains nitrogen induced genes after nitrogen addition to nitrogen starved plants (Wang et al., Plant Physiology, June 2003, Vol. 132, pp. 556-567). FUE_(—)505 was found in the cluster of the ARR (Arabidopsis response regulators) which mediate the response of the shoot to cytokinin. Root cytokinin production increase upon nitrogen availability (Yamada et al. FEBS Lett. Vol. 436, pp: 76-80, 1998). Its co-regulation together with ARRs indicates a possible role in the cytokinin response. It is highly likely that constitutive expression of FUE_(—)505 will improve nitrogen utilization and plant growth due to continuous activation of the cytokinin response of the shoot.

Example 2 mRNA Expression of in-Silico Expressed Polynucleotides

mRNA levels are determined using reverse transcription assay followed by quantitative Real-Time PCR (qRT-PCR) analysis. RNA levels are compared between different tissues, developmental stages, growing conditions and/or different genetic backgrounds. A correlation analysis between mRNA levels in different experimental conditions/genetic backgrounds as evidence for the role of the gene in the plant.

Methods

RT-PCR Analysis—

Root and leaves were excised fresh from maize plants grown on 10 liter white buckets filled with Vermiculite Size 3. Buckets were watered with tap water until seeds from a commercial hybrid germinated. During the entire growth period (5 weeks), the plants were irrigated with 2 liter/bucket/day with a solution pH 5.7-5.8 containing 2 mM CaCl₂, 1 mM MgSO₄, 1 mM KH₂PO₄, 7 mM KCl and microelements cocktail. Ammonium nitrate was added at the following concentrations: 5 mM, 0.5 mM, 0.05 mM, 0.005 mM or not at all. For experiments with Potassium nitrate instead of ammonium nitrate, the concentrations were as follow 2 mM CaCl₂, 2 mM MgSO₄, 1 mM KH₂PO₄, 5 mM KCl, and either one of the following concentrations of KNO₃: 5 mM, 1 mM, 0.1 mM, 0.01 mM, maintained to a final concentration of potassium of 10 mM with supplemental concentrations of KCl.

Quantitative Real Time RT-PCR (qRT-PCR)—

To verify the levels of expression, specificity and trait-association, Reverse Transcription followed by quantitative Real-Time PCR (qRTPCR) was effected on total RNA extracted from several parts of the plant including for example mature and juvenile leaves, roots and root meristems, husks, tassels, silks, etc. from plants grown on soil or pots under optimal or nutrient deficient conditions as described above. Messenger RNA (mRNA) levels are measured for all the genes, previously predicted bioinformatically to be associated with Fertilizer Use Efficiency and correlation between expression levels and the plant nutrient status was analysed. Total RNA was extracted from leaves or roots of maize, using RNeasy plant mini kit (Qiagen, Germany) using the protocol provided by the manufacturer. Reverse transcription was performed using 1.5 μg total RNA, using 300 U Super Script II Reverse Transcriptase enzyme (Invitrogen), 225 ng random deoxynucleotide hexamers (Invitrogen), 500 μM dNTPs mix (Takara, Japan), 0.2 volume of ×5 RT buffer (Invitrogen), 0.01M DTT, 60U RNAsin (Promega), DEPC treated DDW was added up to 37.5 RT reactions were incubated for 50 min at 42° C., followed by 70° C. for 15 min. cDNA was diluted 1:20 in Tris EDTA, pH=8. 5 mL of the diluted cDNA was used for qRT-PCR.

Quantitative RT-PCR was performed on cDNA (5 μL), using ×1 SYBR GREEN PCR master mix (Applied Biosystems), forward and reverse primers 0.3 μM each, and DDW was added up to 20 μL. qPCR reaction was performed in a Stratagene MX 3000 real-time PCR machine with the following conditions 50° C. for 2 min, 95° C. for 10 min, 40 times of 95° C. for 15 sec and 1 min at 60° C., followed by 95° C. for 15 sec, 60° C. for 60 sec, and 70 times of 60° C. for 10 sec+0.5° C. increase in each cycle. For each gene, a standard curve is prepared from a pool of RTs from all samples, in 5 dilutions (dilutions—1:60, 1:200, 1:600, 1:2000, 1:10000). The standard curve plot [ct (cycle threshold) vs. log(concentration)] should have R>=0.98 with an efficiency in the range of 100%+/−5%. The levels of expression (Qty) measured in the qPCR were calculated using the efficiency (E) of the amplification reaction and the corresponding C.T. (the cycle at which the samples crossed the threshold) Qty=E^(−C.T.). The dissociation curves obtained were qualified for the absence of non-specific PCR products or primer-dimers. Reactions were repeated at least twice. The calculation method is based on the assumption that the efficiencies of the reactions of the GOI (gene of interest) and of the housekeeping genes are similar.

To normalize the expression level between the different tissues and growing conditions of maize plants, expression of each gene was divided by the geometric mean of the expression of the following four housekeeping genes: Actin (GenBank Acc No AY107106), and RPL19 (GenBank Acc. No. AY103679), Cyclophyllin (GenBank Acc No X68678) and Elongation factor 1 alpha (EF1A, GenBank Acc No AF136823).

TABLE 29  The following primers were used for qRT-PCR analysis: GENE PRIMER/SEQ ID NO:  Actin FORWARD PRIMER: CCTGACTGAACGCGGCTACT/SEQ ID NO: 1344 Actin Reverse primer: CAATGGTGATGACCTGTCCGT/SEQ ID NO: 1345 RPL19 Forward primer: GGAAAGGCAAAGTCTGGCTTG/SEQ ID NO: 1346 RPL19 Reverse primer: GCACGGGACCTAGAGTGAACC/SEQ ID NO: 1347 Cyclophilin Forward GGACAGCTCTCCTAGATCTCTCTGA/SEQ ID NO: 1348 primer: Cyclophilin Reverse CTAAACCGCTAAATTAAACTGCGAG/SEQ ID NO: 1349 primer: EF1A Forward primer: GTGAACATGCTCTCCTTGCGT/SEQ ID NO: 1350 EF1A Reverse primer: ATTTGGGAGTGGTTGCATCC/SEQ ID NO: 1351 FUE_1 Forward Primer ACTTCCACTGCGCGTAGATGA/SEQ ID NO: 1352 FUE_1 Reverse Primer ACGGAATAATGACGATGAACCAC/SEQ ID NO: 1353 FUE_2 Forward Primer CGAGCGACTCAAACCATGC/SEQ ID NO: 1354 FUE_2 Reverse Primer TCTTGGTGATTGAATCCAGCG/SEQ ID NO: 1355 FUE_2_RT_2F GCATGGTGGGTAAGGTTTTCTT/SEQ ID NO: 1356 FUE_2_RT_2R CAATCTTGGTGATTGAATCCAGC/SEQ ID NO: 1357 FUE_3 Forward Primer CACCATCCACGCACTAGTACGT/SEQ ID NO: 1358 FUE_3 Reverse Primer CAGCTAGCCGCTTCGAGAGAT/SEQ ID NO: 1359 FUE_4 Forward Primer AAGACGCCGATCGATACATTG/SEQ ID NO: 1360 FUE_4 Reverse Primer ACGTATTGAGTTCAGTTCTTCATGTGT/SEQ ID NO: 1361 FUE_5 Forward Primer CCATTCAGAGGATATTTGGGTGA/SEQ ID NO: 1362 FUE_5 Reverse Primer AATACTTGCGACCATGTCTATCCA/SEQ ID NO: 1363 FUE_6 Forward Primer CCAGTCCACAATCTCCCTGCC/SEQ ID NO: 1364 FUE_6 Reverse Primer GTCGTGCGCCTGGCCAAAG/SEQ ID NO: 1365 FUE_7 Forward Primer CTGCGGTCAGAAATCTTATCGTC/SEQ ID NO: 1366 FUE_7 Reverse Primer CGAACACAAAATCAGGCGTCT/SEQ ID NO: 1367 FUE_8 Forward Primer CTTCCGGCTGGGTAAGTTTG/SEQ ID NO: 1368 FUE_8 Reverse Primer ATGGTTCAGTGCCGTCTCCT/SEQ ID NO: 1369 FUE_9 Forward Primer AAGAAGAAGCGACACAGCTCAAC/SEQ ID NO: 1370 FUE_9 Reverse Primer GCAGCAGTAGGATGTGCGATC/SEQ ID NO: 1371 FUE_9_RT_2F CAGCTCAACTGCTCAAGGACAG/SEQ ID NO: 1372 FUE_9_RT_2R GGCGCAGCAGTAGGATGTG/SEQ ID NO: 1373 FUE_10 Forward Primer CGATGCCTACAAGAACTACACCG/SEQ ID NO: 1374 FUE_10 Reverse Primer AGTGGTTCTTGTCCGTGTTGAAG/SEQ ID NO: 1375 FUE_10_RT_2F GCCGATGCCTACAAGAACTACAC/SEQ ID NO: 1376 FUE_10_RT_2R TGAAGATGAGGAAATCCCCG/SEQ ID NO: 1377 FUE_12 Forward Primer TCCTGTTACAGATGGCATCCG/SEQ ID NO: 1378 FUE_12 Reverse Primer TCTCTCTCCTTAGTGAAGACGTTCG/SEQ ID NO: 1379 FUE_12_RT_2F AGAATCTTATAAAGCCCTCACATCGT/SEQ ID NO: 1380 FUE_12_RT_2R GATGACACGGGCGAACAGTA/SEQ ID NO: 1381 FUE_13 Forward Primer CCGCCACCTTTCCTACGTAC/SEQ ID NO: 1382 FUE_13 Reverse Primer TCGGTCTATACTCGATTCGAAGC/SEQ ID NO: 1383 FUE_14 Forward Primer TCTGTGTTGCTGATATTCACTCTCCT/SEQ ID NO: 1384 FUE_14 Reverse Primer CCTTACTCTTCATGGTGTCTCTAGCTT/SEQ ID NO: 1385 FUE_15 Forward Primer GGCCGCCTGTTAGGAGCTA/SEQ ID NO: 1386 FUE_15 Reverse Primer CGCCTCACTCCTACCTTCATCT/SEQ ID NO: 1387 FUE_16 Forward Primer AAGAGGCAGTGCTGTTTCCGT/SEQ ID NO: 1388 FUE_16 Reverse Primer GCCAGAATCGAGCATAGACCA/SEQ ID NO: 1389 FUE_17 Forward Primer GCATCAAAGAGTGGTCAATTCACA/SEQ ID NO: 1390 FUE_17 Reverse Primer CACCCTCCTTTGCAGTGCA/SEQ ID NO: 1391 FUE_30 Forward Primer: CCAAGTCGTCTCTTAGTCCGGA/SEQ ID NO: 1392 FUE_30 Reverse Primer: CAGGATGCACGTCTTGCCT/SEQ ID NO: 1393 FUE_31 Forward Primer: ATGTGCAACGACCCTACTAACTCC/SEQ ID NO: 1394 FUE_31 Reverse Primer: TCAGTGTCCTCAGCGCGAT/SEQ ID NO: 1395 FUE_32 Forward Primer: CTCGAGCATCACTCAAACCACTAC/SEQ ID NO: 1396 FUE_32 Reverse Primer: GCCAGGCCCATTGAATCAC/SEQ ID NO: 1397 FUE_33 Forward Primer: CAGCGCTGTATGGTAAAGGTATTG/SEQ ID NO: 1398 FUE_33 Reverse Primer: TGTGTCATGGAGGCTTGCC/SEQ ID NO: 1399 FUE_34 Forward Primer: GCCACCAACTCCATTCAACTTT/SEQ ID NO: 1400 FUE_34 Reverse Primer: CTCTTATTCATGGGCTTAATTGCA/SEQ ID NO: 1401 FUE_35 Forward Primer: GACGCTCTGATTAGGCTAGGGAC/SEQ ID NO: 1402 FUE_35 Reverse Primer: CCCTGCTGTTACGTGGCC/SEQ ID NO: 1403 FUE_36 Forward Primer: TCAGTGAAGATGAGGCTCGCTA/SEQ ID NO: 1404 FUE_36 Reverse Primer: TCCCATCTAGAAGTGTGTTCTCCA/SEQ ID NO: 1405 FUE_37 Forward Primer: TGTGAGCATCAACTCTAACATGGA/SEQ ID NO: 1406 FUE_37 Reverse Primer: TGACATAAATTTCACACATTCACATCA/SEQ ID NO: 1407 FUE_38 Forward Primer: CTATGGAAATTTGTCACCGTGATC/SEQ ID NO: 1408 FUE_38 Reverse Primer: TCGCAAATTTTCACACGAGGT/SEQ ID NO: 1409 FUE_39 Forward Primer: CCGATGAGCTAGGAGAAGTGTTG/SEQ ID NO: 1410 FUE_39 Reverse Primer: TTTGGCCGATTGGGTATGTC/SEQ ID NO: 1411 FUE_40 Forward Primer: ATTGCAGAGAGGGAAAACGTAAGA/SEQ ID NO: 1412 FUE_40 Reverse Primer: AAATCAAACACGTCCAAGAACATC/SEQ ID NO: 1413 FUE_41 Forward Primer: AAATATTTGTCCTATGGGAATGGG/SEQ ID NO: 1414 FUE_41 Reverse Primer: AGTATAATAGTTCTGTCCAAAGTTGCGT/SEQ ID NO: 1415 FUE_42 Forward Primer: GGTTGCGCGCTCTGACTTA/SEQ ID NO: 1416 FUE_42 Reverse Primer: CCAACGACTCGCCTTCCTAAC/SEQ ID NO: 1417 FUE_43 Forward Primer: CTTTGTAAACCAATGCCATCAGTTAG/SEQ ID NO: 1418 FUE_43 Reverse Primer: GCTGGACTCTCTTCACTTCGCT/SEQ ID NO: 1419 FUE_44 Forward Primer: GCACTGATCAATGCCGACTG/SEQ ID NO: 1420 FUE_44 Reverse Primer: AAGGATTGGATCGGATACTTGTAGA/SEQ ID NO: 1421 FUE_45 Forward Primer: TTATCCATGATACCCCGCTGA/SEQ ID NO: 1422 FUE_45 Reverse Primer: GTGCTTGTTGACTTGACGACG/SEQ ID NO: 1423 FUE_46 Forward Primer: AGCAGCCGCTGTGTATAACAAG/SEQ ID NO: 1424 FUE_46 Reverse Primer: GGAAGGGAAAGAGGACGTCAA/SEQ ID NO: 1425 FUE_47 Forward Primer: TGAACCTACTCTTTGGGATAGCTGT/SEQ ID NO: 1426 FUE_47 Reverse Primer: ACGTGGAGAATTACATGCTGATAGTT/SEQ ID NO: 1427 FUE_48 Forward Primer: ACCATTGTTAGTGACTTAATTACCCTCA/SEQ ID NO: 1428 FUE_48 Reverse Primer: CGAAATCGATAGACCACACACG/SEQ ID NO: 1429 FUE_49 Forward Primer: CCCTTCTACAAGCAAATACTCACTCC/SEQ ID NO: 1430 FUE_49 Reverse Primer: GACCCTCTCATCTCTTATTGAACCA/SEQ ID NO: 1431 FUE_50 Forward Primer: GGCGATCCAACGGAGAAGTAG/SEQ ID NO: 1432 FUE_50 Reverse Primer: ACATCGGCAGCACGGAGT/SEQ ID NO: 1433 FUE_51 Forward Primer: CCGGTGCATAAGGAAATACGAG/SEQ ID NO: 1434 FUE_51 Reverse Primer: GACAGATTGAAAACTGCCCCAG/SEQ ID NO: 1435 FUE_52 Forward Primer: GTCGATCATCGCATTCTCCA/SEQ ID NO: 1436 FUE_52 Reverse Primer: TCCTTTCATCGTATCCCCCAT/SEQ ID NO: 1437 FUE_53 Forward Primer: CAGATCTTCTTCTCTCAGCTCCCT/SEQ ID NO: 1438 FUE_53 Reverse Primer: GGGCTGAATCAACGTCGACT/SEQ ID NO: 1439 FUE_54 Forward Primer: GAAGCTGTGGGTCTCAAGGG/SEQ ID NO: 1440 FUE_54 Reverse Primer: AGGTCGGCACGTACTCGG/SEQ ID NO: 1441 FUE_55 Forward Primer: TCTACATCCAGGCTCTCGTTAGC/SEQ ID NO: 1442 FUE_55 Reverse Primer: TTCATCTTCATCAGTAAGACCATCATC/SEQ ID NO: 1443

Results

Real-time RT-PCR analysis provided evidence that the in-silico selected polynucleotide sequences are indeed associated with Nitrogen Use. Although the majority of the genes were chosen because of their association with drought, genes were found to be responsive to the Nitrogen status within the plant suggesting a cross-talk between drought and nutrient deficiency stress. Evidence that the RNA panel used in this assay does reflect genuine changes associated to the nitrogen status can be found FIGS. 3A-D in which known genes associated to nitrogen uptake and assimilation show changes in their expression levels according to the nitrogen fertilizer level used in the irrigation solution. The graphs represent the normalized expression levels found for each gene divided by the level of expression at the highest nitrogen fertilizer concentration used in the irrigation solution. FIGS. 3A and 3B show the results found for two high affinity nitrate and ammonium transporter respectively. As expected, at higher concentrations of the substrate, the expression of the high affinity transporters is downregulated. Conversely, those high affinity transporters, obviously essential at conditions in which the substrate is scarce, are upregulated at low nitrate and ammonium concentrations (see FIGS. 3A and 3B). As expected for two key enzymes in the nitrogen assimilation pathway such as Glutamine Synthase 1C and Glutamine Synthase 2, their expression is upregulated under high substrate conditions as shown in FIGS. 3C and 3D, respectively. Typically, low affinity transporters are upregulated with high N concentration. Conversely, high affinity transporters are upregulated with low N concentration. Enzymes involved in N-assimilation (the conversion of n to amino acids) are upregulated inn the presence of nitrogen. The genes identified in Example 1 show the distinctive nitrogen responsive behavior found for the control genes (FIGS. 3A-D). FUE_(—)3 (as shown in FIG. 4A) shows upregulation at high substrate concentrations as found for the key control assimilation enzymes indicating a clear association of this gene with the nitrogen status of the plant and hence its relation to nitrogen related-responses. The same upregulation found for FUE_(—)3 was found several other genes included in Example 1 such as FUE_(—)12 (as shown in FIG. 4B), FUE_(—)30 (as shown in FIG. 4C), FUE_(—)33 (as shown in FIG. 4D), FUE_(—)34 (as shown in FIG. 4E), FUE_(—)38 (as shown in FIG. 4F), FUE_(—)43 (as shown in FIG. 4G), FUE_(—)47 (as shown in FIG. 4H), FUE_(—)48 (as shown in FIG. 4I), FUE_(—)49 (as shown in FIG. 4J) and FUE_(—)52 (as shown in FIG. 4K).

Then again, included in Example 1 are genes that show a tight upregulation when nitrogen fertilizer is in short supply. This kind of genes is expected to be related to pathways involved in nitrogen assimilation, storage and use under conditions of nitrogen deficiency as is the case of the high affinity nitrate and ammonium transporters (FIGS. 2C and 2D). FIG. 5A shows the results for FUE_(—)4, a gene that undergoes a strong upregulation at low nitrogen fertilizer availability, indicating a clear role of this gene in the plant endogenous response to nitrogen deficient conditions. Likewise, other genes in Example 1, display a similar nitrogen-responsiveness curve as FUE_(—)4 such as FUE_(—)10 (as shown in FIG. 5B), FUE_(—)37 (as shown in FIG. 5C), FUE_(—)46 (as shown in FIG. 5D) and FUE_(—)50 (as shown in FIG. 5E).

Taken together, the results presented herein clearly imply a close correlation between the in-silico selected genes and nitrogen associated pathways.

Example 3 Gene Cloning and Creation of Binary Vectors for Plant Expression

Cloning Strategy

Twenty eight genes of the 50 genes selected in Example 1 and validated in Example 2 above were cloned into binary vectors for the generation of transgenic plants. For cloning, the full-length open reading frame (ORF) was first identified. EST clusters and in some cases mRNA sequences were analyzed to identify the entire open reading frame by comparing the results of several translation algorithms to known proteins from other plant species. In case where the entire coding sequence was not found, RACE kits from Ambion or Clontech (RACE=Rapid Access to cDNA Ends) were used to prepare RNA from the plant samples described in Example 2 above to thereby access the full cDNA transcript of the gene.

In order to clone the full-length cDNAs, Reverse Transcription followed by PCR(RT-PCR) was performed on total RNA extracted from leaves, roots or other plant tissues, growing under either normal or nutrient deficient conditions. Total RNA extraction, production of cDNA and PCR amplification was performed using standard protocols described elsewhere (Sambrook J., E. F. Fritsch, and T. Maniatis. 1989. Molecular Cloning. A Laboratory Manual., 2nd Ed. Cold Spring Harbor Laboratory Press, New York.) and are basic for those skilled in the art. PCR products were purified using PCR purification kit (Qiagen) and sequencing of the amplified PCR products is performed, using ABI 377 sequencer (Applied Biosystems).

To facilitate cloning of the cDNAs, a 8-12 bp extension was added to the 5′ prime end of each primer. The primer extension includes an endonuclease restriction site. The restriction sites are selected using two parameters: a. The site does not exist in the cDNA sequence. b. The restriction sites in the forward and reverse primers are designed so the digested cDNA is inserted in the sense formation into the binary vector utilized for transformation. For instance, the pPI plasmid vector was constructed by inserting a synthetic poly-(A) signal sequence, originating from pGL3 basic plasmid vector (Promega, Acc. No. U47295; by 4658-4811) into the HindIII restriction site of the binary vector pBI101.3 (Clontech, Acc. No. U12640).

PCR products were purified (PCR Purification Kit, Qiagen, Germany) and digested with the restriction sites according to the primers used (Roche, Switzerland). The digested PCR products were cloned into the binary vector pPI, which was digested with the same restriction enzymes. The digested PCR product and the linearized plasmid vector were ligated using T4 DNA ligase enzyme (Roche, Switzerland). The following genes were cloned from RNA extracted from the tissues described above using the following primers:

TABLE 30  genes cloned from cDNA libraries and the primers used for the cloning Restriction Enzymes Gene used for Name cloning Primers used for amplification/SEQ ID NO: FUE_501 SmaI, Fwd-AACCCGGGAACAATGACACCACAGATCAAAACTCA/ EcoRV SEQ ID NO: 1444 Rev-AGGATATCATATGAATGCTACGGCAAGC/SEQ ID NO: 1445 FUE_502 SmaI, Fwd-AAACCCGGGAACAATGAGGTACGATCAGGAAGCGG/ SacI SEQ ID NO: 1446 Rev-TTGAGCTCGTTCGCTGGAGGTAACAATG/ SEQ ID NO: 1447 FUE_503 SmaI, Fwd-AACCCGGGAACAATGGATCAAAAAGTTAGACAGTT/ EcoRV SEQ ID NO: 1448 Rev-TTGATATCCACAAAACTCTCTAGCTCCTGAC/SEQ ID NO: 1449 FUE_504 XbaI, Fwd-AAACCCGGGAACAATGGAGGACAAGAACAATGATAAG/ SacI SEQ ID NO: 1450 Rev-TTGAGCTCGGGTCTCTTTGTCATGGAGTTC/ SEQ ID NO: 1451 FUE_33 SmaI, Fwd-CTCCCGGGAACAATGGCTCTCGTGACCTCGG/ SacI SEQ ID NO: 1452 Rev-TTGAGCTCCGCAACACAGTTTCATGACCA/ SEQ ID NO: 1453 FUE_34_ XbaI, Fwd-GGTCTAGAAACAATGGGGAGGGGAAAGAT/ Evo EcoRV SEQ ID NO: 1454 Rev-CGGGATATCATAAGACGCCAGTTTTACTCTTATTCATGGGC/ SEQ ID NO: 1455 FUE_34_ XbaI, Fwd-GGTCTAGAAACAATGGGGAGGGGAAAGAT/ Pat EcoRV SEQ ID NO: 1456 Rev-CGGGATATCATAAGACGCCAGTTTTACTCTTATTCATGGGC/ SEQ ID NO: 1457 FUE_39 XbaI, Fwd-AATCTAGAATGGTGGACTTTGTTCGACGG/SEQ SacI ID NO: 1458 Rev-CTGAGCTCACAGGAGGACATGCCACC/SEQ ID NO: 1459 FUE_43 XbaI, Fwd-CATCTAGAAACAATGGCGGACTCGTCGGCG/SEQ SacI ID NO: 1460 Rev-TTGAGCTCGCAGTGTGCAAGAGTTCCCTC/SEQ ID NO: 1461 FUE_50 XbaI, Fwd-AATCTAGAGTAATAAGCCAACAAACAAACCG/SEQ EcoRV ID NO: 1462 Rev-CAGATATCCTAGCATACCGACCCTGAAAACAC/ SEQ ID NO: 1463

Synthetic sequences of some of the cloned polynucleotides were ordered from a commercial supplier (GeneArt, GmbH). The synthetic DNA was designed in silico, based on the putative encoded polypeptide sequences described in Example 1.

To optimize the coding sequence, codon-usage tables calculated from plant transcriptomes were used (example of such tables can be found in the Codon Usage Database available online at Hypertext Transfer Protocol://World Wide Web (dot) kazusa (dot) or (dot) jp/codon/). The optimized coding sequences were designed in a way that no changes are introduced in the encoded amino acid sequence while using codons preferred for expression in dicotyledonous plants mainly tomato and Arabidopsis; and monocotyledonous plants such as maize. Such optimized sequences promote better translation rate and therefore higher protein expression levels. To the optimized sequences flanking additional unique restriction enzymes sites were added-SalI, XbaI, BamHI, SmaI at the 5′ end and Sad at the 3′ end. The genes for which codon optimized synthetic sequences were prepared were: FUE_(—)2 (SEQ ID NO: 1317), FUE_(—)3, (SEQ ID NO: 1319) FUE_(—)4 (SEQ ID NO: 1320), FUE_(—)40 (SEQ ID NO: 1321), FUE_(—)7 (SEQ ID NO: 1322), FUE_(—)8 (SEQ ID NO: 1324), FUE_(—)9 (SEQ ID NO: 1325), FUE_(—)10 (SEQ ID NO: 1326), FUE_(—)12 (SEQ ID NO: 1327), FUE_(—)13 (SEQ ID NO: 1328), FUE_(—)14 (SEQ ID NO: 1329), FUE_(—)16 (SEQ ID NO: 1330), FUE_(—)37 (SEQ ID NO: 1331), FUE_(—)41 (SEQ ID NO: 1332), FUE_(—)46 (SEQ ID NO: 1333), FUE_(—)47 (SEQ ID NO: 1334), FUE_(—)49 (SEQ ID NO: 1335), FUE_(—)52 (SEQ ID NO: 1336).

Two non-optimized sequences, designated “FUE_(—)2_Original” (SEQ ID NO: 1318) and “FUE_(—)7_Original” (SEQ ID NO: 1323), identical to their endogenous maize sequences were synthesized and cloned for overexpression in transgenic plant creation.

Generation of Binary Vectors Comprising FUE Genes and Plant Functional Promoters for Driving Expression of Same—

The plasmid pPI was constructed by inserting a synthetic poly-(A) signal sequence, originating from pGL3 basic plasmid vector (Promega, Acc No U47295; by 4658-4811) into the HindIII restriction site of the binary vector pBI101.3 (Clontech, Acc. No. U12640). In some cases the backbone binary plasmid used was pGI which is similar to pPI but the GUS gene was replaced by the GUS-Intron gene (Vancanneyt. G, et al MGG 220, 245-50, 1990). pGI was used to clone all the polynucleotide sequences, initially under the control of 35S promoter [Odell, J T, et al. Nature 313, 810-812 (28 Feb. 1985); SEQ ID NO: 1337].

Some polynucleotide sequences were cloned under other preferential promoters as described below. One of the promoters, named here “RootP” (SEQ ID NO: 1338) because of its enriched expression in roots, was amplified and cloned from genomic DNA isolated from Arabidopsis thaliana by direct PCR using the following primers.

TABLE 31  Primer name Primer sequence/SEQ ID NO: Root_P Forward TATGTCGACTCAGATGAAGAAGGCGGCT/ (Enzyme SalI) SEQ ID NO: 1464 Root_P Reverse GTCCCGGGTTTATTAGATCTCTCTAGGAG (Enzyne SmaI) TTTTGA/SEQ ID NO: 1465

The promoter is the 1110 bp upstream region of the gene ATXTH19 (AT4G30290, Xyloglucan endotransglucosylase/hydrolase 19). The sequence cloned was already shown to drive root-specific expression (Vissenberg K, et al. Plant Cell Physiol. 2005 January; 46(1):192-200). The following genes were cloned downstream of the RootP promoter sequence: FUE_(—)3, FUE_(—)4, FUE_(—)8, FUE_(—)9, FUE_(—)13, FUE_(—)14, FUE_(—)16, FUE_(—)33, FUE_(—)34_Evo. For control purposes, the β-glucuronidase enzyme (GUS) encoded by the uid A gene (GENBANK ACCESSION NO: S69414).

The TT105 promoter (SEQ ID NO: 1339; 2004/081173) was used to mediate constitutive ubiquitous expression at levels different from those mediated by the 35S promoter. The promoter TT105 contains the upstream region of the ELP gene (Ectopic deposition of Lignin, GENBANK ACCESSION NO: NM_(—)100466, AT1G05850) including the first exon and part of the first intron. The genes cloned under the TT105 promoter were FUE_(—)502, FUE_(—)504, FUE_(—)39 and FUE_(—)52. Here again the β-glucuronidase enzyme (GUS) encoded by the uid A gene was cloned under the TT105 promoter.

Example 4 Generation of Transgenic Plants Expressing the FUE Genes

Materials and Methods

Arabidoposis Transformation—

was effected according to Clough S J, Bent A F. (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16(6): 735-43; and Desfeux C, Clough S J, Bent A F. (20000 Female reproductive tissues are the primary targets of Agrobacterium-mediated transformation by the Arabidopsis floral-dip method. Plant Physiol. 123(3): 895-904.). Briefly—Arabidopsis thaliana var Columbia (T₀ plants) were transformed using the Floral Dip procedure described by Clough S J and Bent A F (10) and by Desfeux C et al. (11), with minor modifications. Briefly, Arabidopsis thaliana Columbia (Col0) T₀ Plants were sown in 250 ml pots filled with wet peat-based growth mix. The pots were covered with aluminum foil and a plastic dome, kept at 4° C. for 3-4 days, then uncovered and incubated in a growth chamber at 18-24° C. under 16/8 hr light/dark cycles. The T₀ plants were ready for transformation six days prior to anthesis. Single colonies of Agrobacterium carrying the binary vectors harboring the FUE genes were cultured in LB medium supplemented with kanamycin (50 mg/L) and gentamycin (50 mg/L). The cultures were incubated at 28° C. for 48 hrs under vigorous shaking and centrifuged at 4000 rpm for 5 minutes. The pellets comprising Agrobacterium cells were resuspended in a transformation medium which contained half-strength (2.15 g/L) Murashige-Skoog (Duchefa); 0.044 μM benzylamino purine (Sigma); 112 μg/L B5 Gambourg vitamins (Sigma); 5% sucrose; and 0.2 ml/L Silwet L-77 (OSI Specialists, CT) in double-distilled water, at pH of 5.7.

Transformation of T₀ plants was performed by inverting each plant into an Agrobacterium suspension such that the flowering stem was submerged for 3-5 seconds. Each inoculated T₀ plant was immediately placed in a plastic tray, then covered with clear plastic dome to maintain humidity and kept in the dark at room temperature for 18 hrs to facilitate infection and transformation. Transformed (transgenic) plants are then uncovered and transferred to a greenhouse for recovery and maturation. The transgenic T₀ plants were grown in the greenhouse for 3-5 weeks until siliques were brown and dry, then seeds were harvested from plants and kept at room temperature until sowing.

For generating T1 and T₂ transgenic plants harboring the genes, seeds collected from transgenic T₀ plants were surface-sterilized by soaking in 70% ethanol for 1 minute, followed by soaking in 5% sodium hypochlorite and 0.05% Triton X-100 for 5 minutes. The surface-sterilized seeds were thoroughly washed in sterile distilled water then placed on culture plates containing half-strength Murashige-Skoog (Duchefa); 2% sucrose; 0.8% plant agar; 50 mM kanamycin; and 200 mM carbenicylin (Duchefa). The culture plates were incubated at 4° C. for 48 hours then transferred to a growth room at 25° C. for an additional week of incubation. Vital T₁ Arabidopsis plants were transferred to fresh culture plates for another week of incubation. Following incubation the T₁ plants were removed from culture plates and planted in growth mix contained in 250 ml pots. The transgenic plants were allowed to grow in a greenhouse to maturity. Seeds harvested from T₁ plants were cultured and grown to maturity as T₂ plants under the same conditions as used for culturing and growing the T₁ plants. At least 10 independent transformation events were created from each construct for which bulk of T2 seeds were collected.

Maize Transformation—

This procedure is done according to (Bronwyn R. Frame, et al, Agrobacterium tumefaciens-Mediated Transformation of Maize Embryos Using a Standard Binary Vector System, Plant Physiology, May 2002, Vol. 129, pp. 13-22) or to the several protocols available elsewhere from the Plant Transformation Facility at Iowa State University (Hypertext Transfer Protocol://World Wide Web (dot) agron (dot) iastate (dot) edu/ptf/Web/mainframe (dot) htm).

Example 5 Selection of Transgenic Arabidopsis Plants Expressing the FUE Genes According to Expression Level

Materials and Methods

Transgenic plants were grown as detailed in Example 4 above. Total RNA was extracted from 10 freshly excised flowers from the transgenic plants as detailed in Example 2 above. In order to determine the relative expression level of the transgene qRT-PCR reactions were performed as described in Example 2 above and the results were normalized against the geometric mean of the expression of two housekeeping genes measured in the same samples.

TABLE 31  Primers used for selection of transgenic plants PRIMER NAME PRIMER SEQUENCE/SEQ ID NO:  NUE10_RT_F CCACTCTGTGGTTCAGACTAGGAAC/SEQ ID NO: 1466 NUE10_RT_R CATTCAACAGTATCATCTGGCCC/SEQ ID NO: 1467 NUE16_RT_F CAGGATGGTCTAGTGGAGTGGAT/SEQ ID NO: 1468 NUE16_RT_R GCAGAGTACTGGAACACAAGGTTATC/SEQ ID NO: 1469 NUE41_RT_F CGTAAGAGAGTGGGACTTACTGGAT/SEQ ID NO: 1470 NUE41_RT_R CCATGCCTATCAGAGTACCTGTGA/SEQ ID NO: 1471 FUE501_RT_F GTCCTGCGTAGACGAGTCGAA/SEQ ID NO: 1472 FUE501_RT_R AGCTTATGACAACAAATAGAACCGC/SEQ ID NO: 1473 NUE50_RT_F GCCACCATTGTACTCGTCCC/SEQ ID NO: 1474 NUE50_RT_R GAAGCCCGTCAGTCCAAGG/SEQ ID NO: 1475 NUE50_RT2_F CCAGTGCATGTACTACCAAGGG/SEQ ID NO: 1476 NUE50_RT2_R CTAGGCCGACTGATGCCG/SEQ ID NO: 1477 FUE501_RT2_F ACTTACGCCGGAGTTATGAAAGAG/SEQ ID NO: 1478 FUE501_RT2_R AAAAGTAGCAACCATCGTAGCAATC/SEQ ID NO: 1479 FUE502_RT_751F CTAGAGGCTAAATACAAAGACAAGTTCG/SEQ ID NO: 1480 FUE502_RT_831R GAACGCACCGTACATGATCG/SEQ ID NO: 1481 FUE503_RT_349F TTATCTTTATCTACTGGTGCGTTATTGC/SEQ ID NO: 1482 FUE503_RT_430R ACGTCGAATGAGGCTTACACG/SEQ ID NO: 1483 FUE504_RT_296F CCAGCAGAAGTAATTTAGATGTTGAGTC/SEQ ID NO: 1484 FUE504_RT_431R CCACCAATGGGCAATTCC/SEQ ID NO: 1485 NUE39_RT2_f GATAAGGAGGAATGGCGCAG/SEQ ID NO: 1486 NUE39_RT2_R GCATCCTCTACTTGAGAGTTGAACAC/SEQ ID NO: 1487 NUE3_RT_F CAACTTACTCCATGCGCTGGT/SEQ ID NO: 1488 NUE3_RT_R GGCTGTTGTTCCTTAAGCCTAGAG/SEQ ID NO: 1489 NUE4_RT_F ATGTTGTTTGGCCAGCAGGT/SEQ ID NO: 1490 NUE4_RT_R AAGTGGAACAGCGTGTGCTCT/SEQ ID NO: 1491 NUE49_RT_F CCACAATCTTACCGTGAGACCA/SEQ ID NO: 1492 NUE49_RT_R GTACTTAGAGGTAGATGACCCGAGGT/SEQ ID NO: 1493 NUE13_RT_F TGAGAGAATGTGGAAGGTTGCAT/SEQ ID NO: 1494 NUE13_RT_R TCATGGTAGTCACAGATCCTGGTC/SEQ ID NO: 1495 NUE2-Original_F AGTGTTCGTCCTCCCAGCAC/SEQ ID NO: 1496 NUE2-Original_R CCTGCCTTTTCTGGATGTCAAC/SEQ ID NO: 1497 NUE7_RT_F TTCTCAACAGGGTGATGATGCT/SEQ ID NO: 1498 NUE7_RT_R GTCTGAACAGTCTTGGTAACAGTCTCTT/SEQ ID NO: 1499 NUE7_Original_ TTGTGTTGGGCGTGAGCA/SEQ ID NO: RT_F 1500 NUE7_Original_ GGGAGGTGGAAGCAAGGC/SEQ ID NO: RT_R 1501 NUE9_RT_F AATGGCTTTCGAGGGACCA/SEQ ID NO: 1502 NUE9_RT_R GGAGAACAAAGTAGATCTGCCCA/SEQ ID NO: 1503 G3PD_RT_F CCTTGACATTGTTTCCAACGCTA/SEQ ID NO: 1504 G3PD_RT_R GACAGTGGTCATGAGTCCCTCA/SEQ ID NO: 1505 UBQ4_RT_F CTTCTGAGCTTTTGTGATGTGATCA/SEQ ID NO: 1506 UBQ4_RT_R ATAAGTTTTTCCCGCAGACCG/SEQ ID NO: 1507 NUE52_RT_F AGCCAAAGACCTTCGCTAACG/SEQ ID NO: 1508 NUE52_RT_R CCAGTCCTAGAGAAAGTGTATGGGA/SEQ ID NO: 1509 GUS_RT2_F GTGTGGGTCAATAATCAGGAAGTG/SEQ ID NO: 1510 GUS_RT2_R AATAACATACGGCGTGACATCG/SEQ ID NO: 1511

Results

About twelve transgenic events were screened for each construct. The results were highly repetitive and showed that within 12 random transformation events about 20 to 40 fold differences in transgene expression were found. Representative examples of such findings are shown in Tables 32, 33, and 34). Based on these findings about 5 different events showing expression levels higher than the median were taken for further gene function validation (see Examples 6-9).

TABLE 32 Normalized Expression level Results found for Expression relative to lowest NUE 43 level expression level found FUE_43 Event 1 0.1503277 1 FUE_43 Event 2 0.16169295 1.075603188 FUE_43 Event 3 0.48948083 3.256092124 FUE_43 Event 4 0.62021826 4.12577504 FUE_43 Event 5 0.65818337 4.378324085 FUE_43 Event 6 0.66609819 4.430974496 FUE_43 Event 7 0.77390675 5.148131499 FUE_43 Event 8 0.88588004 5.892992865 FUE_43 Event 9 1.47644781 9.821528908 FUE_43 Event 10 3.35576541 22.32300168

TABLE 33 Normalized Expression level Results found for Expression relative to lowest NUE 49 level expression level found FUE_49 Event 1 0.284411514 1 FUE_49 Event 2 0.40568304 1.426394573 FUE_49 Event 3 0.523973448 1.842307439 FUE_49 Event 4 0.606977918 2.134153816 FUE_49 Event 5 0.747036597 2.626604621 FUE_49 Event 6 0.763272592 2.6836909 FUE_49 Event 7 1.057302538 3.717509615 FUE_49 Event 8 1.28937008 4.533466532 FUE_49 Event 9 1.572327678 5.528354517 FUE_49 Event 10 1.750374095 6.154371426 FUE_49 Event 11 4.491236228 15.79133054 FUE_49 Event 12 10.44746677 36.73362806

TABLE 34 Normalized Expression level Results found for Expression relative to lowest NUE 16 level expression level found FUE_16 Event 1 0.143683 1 FUE_16 Event 2 0.884513 6.156021 FUE_16 Event 3 0.975626 6.790146 FUE_16 Event 4 1.05558 7.346604 FUE_16 Event 5 1.296067 9.020344 FUE_16 Event 6 1.550371 10.79025 FUE_16 Event 7 2.161574 15.04409 FUE_16 Event 8 2.918563 20.31257 FUE_16 Event 9 3.126949 21.76289 FUE_16 Event 10 3.149679 21.92108 FUE_16 Event 11 5.041681 35.089

Example 6 Improved Fertilizer Use Efficiency in Tissue Culture Assay

Materials and Methods

Assay 1: Nitrogen Use Efficiency Assay Using Plantlets—

The assay was done according to Yanagisawa-S. et al. with minor modifications (“Metabolic engineering with Dof1 transcription factor in plants: Improved nitrogen assimilation and growth under low-nitrogen conditions” Proc. Natl. Acad. Sci. USA 101, 7833-7838).

Transgenic plants which were grown for 7-10 days in 0.5×MS [Murashige-Skoog] supplemented with a selection agent were transferred to two nitrogen-limiting conditions: MS media in which the combined nitrogen concentration (NH₄NO₃ and KNO₃) was 0.2 mM or 0.05 mM. Plants were allowed to grow for additional 30-40 days and then photographed, individually removed from the Agar (the shoot without the roots) and immediately weighed (fresh weight) for later statistical analysis. Constructs for which only T1 seeds were available were sown on selective media and at least 25 seedlings (each one representing an independent transformation event) were carefully transferred to the nitrogen-limiting media. For constructs for which T2 seeds were available, different transformation events were analyzed. Usually, 25 randomly selected plants from each event were transferred to the nitrogen-limiting media allowed to grow for 3-4 additional weeks and individually weighed at the end of that period. Transgenic plants were compared to control plants grown in parallel under the same conditions. Mock-transgenic plants expressing the uidA reporter gene (GUS) under the same promoter were used as control.

Statistical Analyses—

To identify genes conferring significantly improved nitrogen use efficiency (or tolerance to abiotic stresses or enlarged root architecture, see below) the results obtained from the transgenic plants were compared to those obtained from control plants. Plant area data, seed weight data and plant weight data were analyzed using one-way ANOVA. To identify outperforming genes and constructs, results from the independent transformation events tested were analyzed separately. In addition, genes and constructs were also analyzed taking into consideration the results obtained from all the independent transformation events tested the specific construct. For gene versus control analysis Student's t test or Tukey HSD test were applied, using significance of p<0.05. The JMP statistics software package was used (Version 5.2.1, SAS Institute Inc., Cary, N.C., USA). The same statistical analysis was used in Examples 6-9 which follow.

Results

Polynucleotide sequences of the present invention were assayed for a number of commercially desired traits.

FIG. 7 shows the ability FUE_(—)504 or FUE_(—)39 to improve NUE of transgenic plants expressing same. Clearly the transgenic plants grown on nitrogen are bigger and heavier than control plants expressing a control gene under the same promoter used to express the transgenes. To verify that the increase in the mass achieved by the transgenic plants is statistically significant, plants were individually weighed and the results of the entire population of events analyzed. As shown in Table 35 below transgenic plants expressing FUE_(—)504 are significantly heavier than the control counterparts. The results demonstrate an improvement in NUE since the transgenic plants expressing FUE_(—)504 are able to produce significantly more biomass than control plants starting from a similar nitrogen poor-media.

TABLE 35 Nitrogen conc. Least Sq Mean weight (mg) Std Error 0.2 mM Candidate 1 5.5185185* 0.3626 0.2 mM Control 3.032 0.3769 *results are significantly different at = 0.05

Notably, whenever T1 plants were used to assay the effect of FUE_(—)504; therefore each plant tested is a result of a different transformation event. Having this in mind it is clear that the effect found for T1 plants is a result of the transgene which is not associated with the transgene integration site. When T2 plants were assayed, the results were reproducible whereby in three independent transformation increased fresh weight was evident under limiting nitrogen conditions. Similar results were obtained for FUE_(—)39 and FUE_(—)52. As shown in Table 36 below three independent transgenic events contributed to the increase of the plantlet biomass under limiting nitrogen conditions. The results indicate that the expression of also FUE_(—)39 and FUE_(—)502 induces a significant improvement in nitrogen use efficiency.

TABLE 36 Least square means of fresh weight measured from ~25 plantlets grown for 30 days in 0.05 mM combined nitrogen concentration (NH₄NO₃ and KNO₃) (results analyzed using Student's t test) Level Least Sq Mean TT105::FUE_52 Event 1 A 6.8000000 TT105::FUE_39 Event 1 A B 6.5352941 TT105::FUE_52 Event 2 B C 5.6272727 TT105::FUE_39 Event 2 B C 5.6240000 TT105::FUE_504 Event 1 B C 5.5956522 TT105::FUE_39 Event 3 C D 5.4400000 TT105::FUE_504 Event 2 C D 5.1666667 TT105::FUE_52 Event 3 C D E 5.1473684 TT105::FUE_504 Event 3 C D E 4.8882353 TT105::GUS F G H I 3.6458333 Levels not connected by same letter are significantly different

Similar results were obtained when checking the same events at 0.2 mM combined nitrogen concentration. Four events transformed with TT105::NUE_(—)39 produced statistically significant higher biomass when compared to control plants. Similar results were obtained with 3 events transformed with TT105::NUE_(—)52 and 2 events transformed with TT105::NUE_(—)504 as shown in Table 37.

TABLE 37 Least square means of fresh weight measured from ~25 plantlets grown for 30 days in 0.2 mM combined nitrogen concentration (NH₄NO₃ and KNO₃) (results analyzed using Student's t test) Level Least Sq Mean TT105::FUE_504 Event 1 A 7.5250000 TT105::FUE_52 Event 1 A B 7.4571429 TT105::FUE_39 Event 1 A B 7.2000000 TT105::FUE_39 Event 2 A B C 6.7312500 TT105::FUE_39 Event 3 A B C D 6.6000000 TT105::FUE_52 Event 2 A B C D 6.5869565 TT105::FUE_504 Event 2 B C D E 6.3280000 TT105::FUE_39 Event 4 C D E F 5.8454545 TT105::GUS (CONTROL) G H I J 4.5720000 Levels not connected by same letter are significanty different

Positive results were also obtained in an assay performed using T1 seeds of transgenic plants overexpressing either FUE_(—)8, FUE_(—)14 or FUE_(—)40 under a constitutive ubiquitous promoter (35S), as shown in Table 38 below.

TABLE 38 Least square means of fresh weight measured from ~25 plantlets grown for 27 days in 0.05 and 0.2 mM combined nitrogen concentration (NH₄NO₃ and KNO₃) (results analyzed using Student's t test MANOVA) Level Least Sq Mean 35S::FUE_14 B 6.614423 35S::FUE_40 B C 5.552381 35S::FUE_8 C 5.252 35S::GUS Event 1 D E F 4.217095 35S::GUS Event 2 F 3.27 Levels not connected by same letter are significantly different

Similar results were obtained for different events of other constructs expressing FUE genes. An additional construct bearing the FUE_(—)39 gene under the 35S promoter was checked using this assay as shown in the Table 39 below. In addition, two independent transformation events overexpressing the FUE_(—)49 gene and additional events transformed with either FUE_(—)4, FUE_(—)3, or FUE_(—)43 showed significantly higher biomass produced at both nitrogen limiting conditions tested as shown in table 39 below.

TABLE 39 Least square means of fresh weight measured from ~25 plantlets grown for 27 days in 0.05 and 0.2 mM combined nitrogen concentration (NH₄NO₃ and KNO₃) (results analyzed using Student's t test MANOVA) Level Least Sq Mean 35S::FUE_43 event 1 A 5.572 35S::FUE_49 event 1 A B 5.025 35S::FUE_3 event 1 A B 4.924 5134.1 A B C 4.7 35S::FUE_49 event 2 A B C D 4.512 35S::FUE_4 event 1 A B C D E 4.383333 wild type F G H I J K L 3.123944 35S::GUS H I J K L M N O P 2.702041 Levels not connected by same letter are significantly different

Taking into account the results obtained using this assay, several FUE genes have shown their ability to induce a significant improvement in nitrogen use efficiency. The genes that showed significant results are: FUE_(—)504, FUE_(—)39, FUE_(—)52, FUE_(—)502, as well as the following group of genes: FUE_(—)14, FUE_(—)8, FUE_(—)40 and FUE_(—)49, FUE_(—)3, FUE_(—)4 and FUE_(—)43.

Assay 2: Nitrogen Use Efficiency Whole Plant Assay: Growth Rate at Limited Nitrogen Concentration—

An additional assay designed to identify improved nitrogen use efficiency was developed. This assay follows the rosette area growth of plants grown in the greenhouse at limited nitrogen availability. Surface sterilized seeds were sown and plants grown at 25° C. under 23-hour light 1-hour dark daily cycles for 7-10 days in 0.5× Murashige-Skoog medium in the presence of 2% sucrose. Then seedlings of similar size were carefully transferred to 100 ml pots filled with an inert growth medium support (a fine perlite mix). Seedlings were allowed to develop for a further week irrigated with a solution containing abundant supply of micro and macronutrients. Fertilizer excess was washed from the pots with at least two volumes of low-nitrate tap water. Then, plants were individually inspected and only healthy plants were chosen for growth rate analysis. The chosen plants were randomly distributed in several trays and used to assay for growth rate analysis under nitrogen limiting conditions. Constant nitrogen limiting conditions were achieved irrigating the plants with a solution containing 0.5 mM inorganic nitrogen (combined KNO₃ and NH₄NO₃ concentration), supplemented with 2 mM CaCl₂, 1.25 mM KH₂PO₄, 1.50 mM MgSO₄, 5 mM KCl, 0.01 mM H₃BO₃ and microelements. To follow plant growth, trays were photographed the day nitrogen limiting conditions were initiated and subsequently every 2-3 days for ˜20 additional days. Rosette plant area was then determined from the digital pictures using the methodology described in FIG. 6. ImageJ software was used for quantifying the plant size from the digital pictures (Hypertext Transfer Protocol://rsb (dot) info (dot) nih (dot) gov/ij/) utilizing proprietary scripts designed to analyze the size of rosette area from individual plants as a function of time. Percentage of growth was calculated as the ratio of the plant rosette area divided by the initial plant area measured at day 1. To identify the transgenic plants within the experiment, the presence of the selection marker gene was checked using PCR. Leaf samples were taken from the plants, genomic DNA was extracted and served as template for a PCR using primers specific for the selection marker gene. Positive plants were tagged in order to exclude from the analysis the non-transgenic plants.

TABLE 40  Primers used for the PCR analysis: Primer name Primer sequence/SEQ ID NO:  NPTII-F CGAGAAAGTATCCATCATGGC/SEQ ID NO: 1512 NPTII-R ATGTCCTGATAGCGGTCCGC/SEQ ID NO: 1513

Results

In agreement with the results obtained in the previous assay in which FUE_(—)39 showed improved NUE, the results presented herein show that FUE_(—)39 significantly improved NUE in whole plants. As shown in Table 41 below, two independent transgenic events expressing FUE_(—)39 were found to display enhanced NUE when compared to either wild type or transgenic plants expressing the GUS reporter gene under the same promoter used to express the FUE_(—)39 transgene.

TABLE 41 FUE_39 shows the results of a growth rate assay under limiting nitrogen conditions. Two events showing enhanced NUE were shown. Level Least Sq Mean 35S::FUE_39 A 867.53380 Event 1 35S::FUE_39 B 685.52595 Event 2 Wild type C D 590.28343 Levels not connected by same letter are significantly different

In addition to FUE_(—)39, also events overexpressing FUE_(—)7 and FUE_(—)41 were found to display enhanced growth rate under limiting nitrogen conditions. As shown in Table 42, FUE_(—)7, FUE_(—)41, FUE_(—)50, FUE_(—)16 expression under the 35S promoter are significantly better than control plants (wild type or expressing a reporter gene under 35S promoter).

TABLE 42 Least Sq Level Mean 5351.3 (35S::FUE_7) A 1184.9559 5375.1 (35S::FUE_41) A 1010.5752 5345.1 (35S::FUE_50) A B  956.9474 5361.2 (35S::FUE16) B C  824.0414 4545.7 (35S::GUS) D E F G H I  515.8663 Levels not connected by same letter are significantly different

Thus, the assay described here follows the ability of the plant to grow at limiting nitrogen conditions. Since the transgenic plants described above developed significantly faster than control plants it can be assumed that the outstanding events were able to assimilate the nitrogen available and to convert it to organic matter. As all the plants in the experiment were treated similarly, the results indicate that the outstanding events were able to utilize more efficiently the nitrogen available and therefore display enhanced nitrogen use efficiency.

Assay 3: Seed Yield Assay at Limited Nitrogen Availability—

Maize plants absorb and store the majority of the nitrogen in leaves and stalk until flowering. Stored nutrients are then redistributed to the developing kernels. In the present assay plants were grown in limited nitrogen conditions as detailed in Assay 2 above for about 45 days and then grown until full maturity with tap water only. Plants are therefore forced to redistribute the stored nitrogen to the developing seeds. Plants that store more nitrogen are expected to have a better yield. Seeds were collected from individual plants and the yield was measured as seed weight. The yield of at least about 6 transgenic plants was usually measured for each event tested.

Results

In this assay transgenic plants overexpressing FUE_(—)43 (under the 35S promoter) were found to have increased seed yield as shown in Table 43. The results of one of the events are presented below.

TABLE 43 Level Least Sq Mean 5151.2 (35s::NUE43) A 0.10411111 4542.4 (35S::GUS) B C D E F G H 0.06647500 Levels not connected by same letter are significantly different

Taken as a whole the results shown here demonstrate that genes from this invention are capable of improving different aspects of nitrogen use efficiency as demonstrated by the results of the different assays disclosed here.

Example 7 Evaluating Transgenic Plant Growth Under Abiotic Stress Conditions

Tolerance to salinity or osmotic stress is aimed at identifying genes that confer better germination, seedling vigor or growth in high salt, drought or combination of same or other environmental stresses. Plants differ in their tolerance to salt stress, high osmoticum and drought during different stages of development. Therefore seed germination, plant development, and yield were evaluated independently under the different stress conditions.

A typical salinity tolerance test is produced taking plants at different developmental stages and irrigating them with increasing concentrations of NaCl (for example 50 mM, 100 mM, 200 mM, 400 mM) or constant concentration of NaCl. Transgenic plants are then compared to control plants in their external phenotypic appearance, degree of wilting, and overall success to reach maturity and yield progeny at concentrations inhibitory to control plants. Quantitative parameters of tolerance measured include, the average wet and dry weight, and the weight of the seeds yielded, the average seed size and the number of seeds produced per plant. Osmotic stress assays (including NaCl and mannitol assays) are conducted to determine if an osmotic stress tolerant phenotype is NaCl-specific or if it is a general osmotic stress related phenotype. Drought assays are performed for example halting irrigation during long period and measuring wilting rate, recovery and final yield. Plants tolerant to osmotic stress are in general more tolerant to drought, salinity and freezing conditions and therefore are highly valuable in terms of agronomic traits.

Materials and Methods

The method used to test the plants for improved abiotic stress tolerance includes the test of germination and seedling growth under adverse conditions such as high salinity and high osmoticum.

Germination Assay Under Abiotic Stresses—

Germination tests compare the percentage of seeds from transgenic plants that could complete the germination process (radicle protrusion from the seed coat and complete opening of the cotyledons) to the percentage of seeds from control plants treated in the same manner. Evaluation of germination and seedling vigor was conducted for three weeks after planting. To measure germination and seedling growth, seeds from T2 plants were surface sterilized and individually sown on square agar plates containing for example, solidified basal media (50% Murashige-Skoog medium (MS)+vitamins supplemented with 0.8% plant agar) supplemented with high salinity (150 mM NaCl) or high osmoticum (210 mM mannitol). After sowing, plates were transferred for 2-3 days at 4° C. for stratification and then grown for three weeks.

To follow the germination and growth at adverse conditions plants were screened manually or automatically and plant size was determined Various independent transformation events selected from Example 5 were analyzed from each construct. Plants expressing the genes from this invention were compared to control plants (wild type or mock-transformed plants) sown on the same plates under the same conditions.

Seedling Growth Under Abiotic Stress—

A complementary experiment performed with seedlings follows the tolerance of the plants to adverse conditions. Surface sterilized seeds were sown in basal media [50% Murashige-Skoog medium (MS)+vitamins supplemented with 0.8% plant agar as solidifying agent] in the presence of Kanamycin (for transgenic plants) or in its absence (for wild-type control plants). After sowing, plates were transferred for 2-3 days at 4° C. for stratification and then grown at 25° C. under 23-hour light 1-hour dark daily cycles for 7 to 10 days. At this time point, seedlings randomly chosen were carefully transferred to plates containing high salinity conditions (150 mM NaCl) or conditions resembling the high osmolarity found during drought (210 mM mannitol). Plant growth was followed as a function of time using digital imaging. To follow the plant growth at adverse conditions plants were photographed the day they were transferred to the stress conditions (Day 1). Pictures were subsequently taken every few days after transferring the plants to the stress condition and up to 12 days after the transfer. Rosette plant area was then determined from the digital pictures. ImageJ software was used for quantifying the plant size from the digital pictures (Hypertext Transfer Protocol://rsb (dot) info (dot) nih (dot) gov/ij/). Proprietary scripts were designed to analyze the size of individual plants rosette areas as a function of time. FIG. 6 shows the methodology used for image area quantification. Five to ten independent transformation events were analyzed from each construct and at least 6 randomly selected plants from each event were analyzed in each stress experiment. Plants expressing the genes from this invention were compared either to control plants sown on the same stress inducing plates (internal controls) or to the average measurement of all the control plants used in the same experiment (all controls).

Results

Salinity and osmoticum tolerance were assayed by following plant growth during stress, as evidenced by plant green area. Several genes and constructs were checked using the procedure described above and significant tolerance results were found. For instance, transgenic plants overexpressing the following genes have shown statistically significant improved tolerance to high salinity stress: FUE_(—)7, FUE_(—)10, FUE_(—)14, FUE_(—)16, FUE_(—)33, FUE_(—)37, FUE_(—)39, FUE_(—)40, FUE_(—)41, FUE_(—)47, FUE_(—)50, FUE_(—)502, FUE_(—)503 and FUE_(—)504.

In addition, the following genes provided statistically significant results in coffering abiotic stress tolerance to the transgenic plants overexpressing same when exposed to high osmolarity stress: FUE_(—)3, FUE_(—)9, FUE_(—)10, FUE_(—)13, FUE_(—)37, FUE_(—)39, FUE_(—)40, FUE_(—)41, FUE_(—)43, FUE_(—)49, FUE_(—)502, FUE_(—)503 and FUE_(—)504.

In addition, transgenic plants expressing FUE_(—)43 and FUE_(—)503 were found to have increased ability to germinate under high osmoticum conditions (Data not shown).

Furthermore, transgenic plants expressing the following genes have shown significantly increased abiotic stress tolerance to either salinity or high osmolarity: FUE_(—)10, FUE_(—)37, FUE_(—)39, FUE_(—)40, FUE_(—)41, FUE_(—)502 and FUE_(—)504.

It should be noted that the significance of the results is in general supported by several transgenic events expressing the above genes and in some cases also under different promoters. Table 44a-b summarize these findings. Results are expressed as the growth area percentage related to the size of the plant when transferred to stress conditions (i.e., Day 1).

TABLE 44a list of genes showing improved seedling growth under salinity stress Gene Promoter Event/Gene Least Sq Mean Salinity Seedling Growth Assay FUE_502 35S 5125.3 A 402.61787 CONTROL B 270.40066 FUE_503 5184.3 A 314.80237 CONTROL B 163.06265 FUE_504 35S 5147.5 A 335.25831 CONTROL B 258.27089 Level TT105 5432.9 A 525.38863 5433.5 A 382.86771 5433.4 A 346.97902 5433.6 A 342.96170 CONTROL B 257.88942 FUE_7 35S 5351.8 A 508.52644 CONTROL B 410.02970 FUE_10 35S 5331.1 A 404.86015 CONTROL B 320.63800 Experiment performed on T1 plants FUE_14 RootP RootP::FUE14 A 239.97813 35S::GUS B 193.74654 35S 5451.3 A 170.50102 5454.1 A 154.77155 5454.4 A B 151.54574 CONTROL C 130.92706 Experiment performed on T1 plants FUE_16 RootP RootP::FUE16 A 184.69992 35S::GUS B 146.24402 Experiment performed on T1 plants FUE_33 RootP RootP::FUE33 A 237.73455 35S::GUS B 202.99142 Experiment performed on T1 plants FUE_37 RootP RootP::FUE37 A 228.14620 35S::GUS B 195.15386 FUE_39 35S 5131.1 A 272.46189 CONTROL B C 195.66170 Experiment performed on T1 plants FUE_40 35S 35S::FUE_40 A 261.52868 35S::GUS B 160.55573 FUE_41 35S 5373.1 A 452.27789 CONTROL B C 373.83060 Experiment performed on T1 plants FUE_47 35S FUE47 A 202.37548 35S::GUS B 142.22673 FUE_50 5343.1 A 452.75078 CONTROL B 376.63355

TABLE 44b list of genes showing improved seedling growth under osmoticum stress Gene Promoter Event/Gene Least Sq Mean Osmoticum Seedling Growth Assay FUE_502 35S 5125.9 A 5125.10 B 156.16627 5125.1 B 145.40683 CONTROL C 92.51323 Experiment performed on T1 plants TT105 TT105::FUE502 A 145.94616 TT105:GUS B 129.39693 FUE_503 5182.3 A 163.93440 5181.2 A 151.83208 CONTROL B 126.70438 Experiment performed on T1 plants FUE_504 TT105 TT105::FUE504 A 172.68759 TT105:GUS B 145.85106 FUE_3 35S 5213.1 A 309.25610 CONTROL B C 244.05079 FUE_9 RootP RootP::FUE9 A 213.03081 35S::GUS B 175.62303 FUE_10 35S 5331.1 A 438.55622 CONTROL B 202.58577 FUE_13 35S 5235.2, 7 A 312.47256 CONTROL, 7 B C 233.04378 Experiment performed on T1 plants RootP RootP::FUE13 A 173.97881 35S::GUS B 134.41030 Experiment performed on T1 plants FUE_37 RootP RootP::FUE37 A 205.43584 35S::GUS B 168.99783 FUE_39 35S 5131.1 A 261.25201 CONTROL B 177.03349 Experiment performed on T1 plants FUE_40 35S 35S::FUE_40 A 142.16470 35S::GUS B 125.81481 FUE_41 35S 5373.2 A 306.74015 5371.4 B 231.50773 CONTROL C 196.22318 FUE_49 35S 5243.3, 7 days A 382.37255 CONTROL, 7 B C 270.81987 days

Example 8 Evaluating Changes in Root Architecture in Transgenic Plants

Many key traits in modern agriculture can be explained by changes in the root architecture. Root size and depth correlates with drought tolerance and fertilizer use efficiency. Deeper root systems can access water in stored in deeper soil layers. Similarly, a highly branched root system provides better coverage of the soil and therefore can effectively absorb all macro and micronutrients available resulting in enhanced fertilizer use efficiency. To test whether the transgenic plants produce a different root structure, plants were grown in agar plates placed vertically. Plates were photographed every few days and the maximal length and total area covered by the plant roots were assessed from the digital pictures. From every construct created, several independent transformation events were checked in replicates. To assess significant differences between root features, one ANOVA using Students t-test was employed in order to identify the events showing outstanding root features and to provide a statistical score to the findings (statistical assays are described above).

Results

When analyzing different aspects of root architecture such as total root area covered and maximal depth (length) achieved by the root system, it was found that transgenic plants expressing FUE genes have remarkable features. For instance, transgenic plants overexpressing FUE_(—)10 and FUE_(—)49 were found to have a higher root area coverage based on measurements done 21 days following germination (see Table 45).

TABLE 45 Root Area (in cm²) measured at day 21 Level Least Sq Mean 21 days 35S::NUE10 A 1.3313852 21 days 35S::NUE49 A 1.3253389 21 days 35S::GUS B C 1.1289837 Levels not connected by same letter are significantly different

Similarly, plants overexpressing FUE_(—)16 and FUE_(—)7 original were found to produce the longest root architecture (see Table 46 below). FUE_(—)16 was found to produce the fastest penetrating root system from all the constructs tested at all days tested (7, 14 and 21 days after germination).

In practice, these findings suggest that plants overexpressing FUE_(—)16 and FUE_(—)7_Original reach deeper soil layers compared to other plants at the same period of time. These plants are expected to maximally retrieve fertilizers and water from the soil and withstand better longer periods of drought.

TABLE 46 Statistical analysis of root length (in cm) measured at day 21 Level Least Sq Mean 21 days 35S::FUE_7_Original A 6.5156396 21 days 35S::FUE_16 A B 6.1808293 21 days 35S::GUS C D 5.5097884 Levels not connected by same letter are significantly different

The enhanced root architecture allows transgenic plants expressing FUE genes to absorb more successfully the nutrients (fertilizers) and water available in the soil.

Increased uptake and nutrient recovery is a key feature for improved fertilizer use efficiency and abiotic stress tolerance. Deeper root systems allow plants to access water available in deeper soil layers enhancing the tolerance to extended drought periods and therefore ensuring high yields also under harsh conditions.

Example 9 FUE_(—)40 Expressing Plants are Characterized by a Plant Architecture for Maximal Seed Production

The presence of multiple seed producing organs (pods, fruits, etc) and strong flowering stems is a key feature to produce high seed yields. While reducing the present invention to practice, the present inventors have surprisingly found that transgenic plants expressing FUE_(—)40 under a constitutive promoter have improved reproductive organ architecture. The flowering stems were unusually stiff and strong and carry a large number of siliques (see FIG. 9 showing different independent transformation events). The results were confirmed by a triple blind assay identifying plants having more siliques per plant, probably due to faster growth of lateral inflorescence shoots. Interestingly, all the plants were different transformation events bearing the same construct, NUE40 gene under 35S promoter (see FIG. 9). This alteration in plant development characteristics can be used to significantly increase seed yield of a plant.

Example 10 CT-9 (SEQ ID NO: 1340, 1341) and CT-71 (SEQ ID NO: 1342, 1343) Confer Drought Tolerance and Increased Yield of Transgenic Tomato

While further reducing the present invention to practice the present inventors have surprisingly uncovered that CT_(—)9 (SEQ ID NOs. 1340, 1341 previously disclosed in PCT Application No. WO2005/121364) and CT_(—)71 (SEQ ID NOs. 1342 and 1343, previously disclosed in PCT Application No. WO2005/121364) confer drought resistance and increased yields in transgenic plants expressing same. CT_(—)9 and CT_(—)71 were disclosed in PCT Application No. WO2005/121364 to Evogene Ltd. and in U.S. Pat. No. 5,597,718 (CT_(—)71).

Materials and Experimental Procedures

Drought Assay—

The drought assay described herein was effected in field conditions mimicking drought stress by controlling the amount of water supplied and the drought intervals. The assay, one source dripping irrigation system (OSDI), is similar to the farmer field since it creates water deficiency in a relatively uniform manner and enables to measure the effect of drought on small size populations of plants.

Thus, the present irrigation method may be effected as follows:

-   -   (a) placing on or in a soil a dripping irrigation system so as         to obtain irrigation holes distributed 20-40 cm (e.g., 30 cm)         from one another in the X and Y directions; and     -   (b) continuously irrigating through each of said irrigation         holes at an irrigation rate of 0.5-2 liter water per hour.

One configuration of an irrigation system (10) for mimicking drought conditions which comprises the following components and illustrated in FIG. 10 may be used in accordance with the teachings of the present invention:

-   -   (i) a dripping irrigation system having a plurality of         irrigation holes (12) distributed 20-40 cm from one another in         the X and Y directions; and     -   (ii) a water supply and control system (14) for continuously         irrigating through each of said irrigation holes 0.5-2 liter         water per hour.

Preferred drippers used are pressure-compensated thick-walled dripper line with anti-siphon and anti-drain systems (UniRam™ CNL #16010, Flow Rate 1.6 l/h from Netafim Israel). Anti-siphon system prevents dirt backflow into the dripper line while anti-drain (CNL) system eliminates drainage and refill effect, and improves efficiency in pulse irrigation.

The OSDI method was developed on the basis of the line source sprinklers irrigation system (Hanks et al. 1976 Soil Sci. Soc Am. J. 40 p. 426-429) with significant modifications. Instead of sprinklers irrigation a dripping irrigation was used. In order to create a uniform and deep wet layer (at least 60 cm depth) and not the onion shape layer that is typically created by dripping irrigation a low pressure compensating dripping irrigation system was used that allow providing small amount of water in a relatively long period of time.

The experiment was created in light soil during summer 2006 (from July to September), in an open field nethouse near Rehovot, Israel.

The water capacity of the soil was measured using the standard procedures by sampling soil from the following three depths: 0 to 20 cm, 20 to 40 cm and 40 to 60 cm. The water content in these soil layers was measured routinely every week. The soil contained 5% hygroscopic water while the maximum water capacity of the soil was 20%. All fertilizers were applied into the soil prior to sowing. The amount of both phosphorus and potassium was calculated to be sufficient for all season. Nitrogen was applied as recommended, equally to all the treatments through the irrigation system.

Each row, 193 cm wide, contained three dripping irrigation lines creating coverage of nine drippers per 1 sq. m. The water control was done separately for each treatment. The soil was dried completely before the beginning of the experiment.

Sowing was done in a nursery conditions under regular water irrigation. The seedlings were transplanted after four weeks into wet soil. The water amount that was used to uniformly irrigate before transplanting reached the maximum water capacity (20% w/w) at 60 cm depth however without creation of water overload. Each plant was transplanted near a dripper, 30 cm distance between plants with a total density of 2600 plants per 1000 sq. m, according to commercial growth protocol. The experiment was structured in four blocks containing three rows irrigated with different water levels and intervals (WLI-0, WLI-1, WLI-2). The different water regimes started only four weeks following transplanting when plants reached the flowering stage. The amount of water supplied every week during the assay was calculated at every beginning of the week following the recommendations of standard growing protocols.

WLI-0 treatment received the recommended total weekly irrigation volume, but divided in three irrigations. The two other treatments (WLI-1 and WLI-2) represent two different level of water deficiency. WLI-1 was also irrigated three times a week, but the amount of water supplied was half of the irrigation supplied to WLI-0. At the end of every week, WLI-1 plants received the amount of water required to reach maximum soil water capacity. WLI-2 was not irrigated during the week but rather at the beginning of every week. Water was supplied to achieve the maximum water capacity. The water stress experiment lasted throughout the flowering period (23 days) corresponding to 4 cycles of the stresses described above. Afterwards, all the treatments received the recommended amount of water.

The calculation of the water amount was equal to the difference between water content in dry soil and soil with maximum water capacity. At the end of each stress cycle the water amount was compared between treatments according to actual water content in the soil (Table 47)

TABLE 47 Water content (%) in the soil at the end of the 4^(th) stress cycle (23 days) Water content in the soil (% w/w) Treatment/Soil depth (cm) Control - WLI-O WLI-1 WLI-2  0-20 17 14 10 20-40 16 12 12 40-60 15 12 11 Of note, during the stress period treatments WLI-1 and WLI-2 received in total 75% less water compared to control (WLI-O).

Gene Cloning and Expression—

Bioinformatic identification, cloning and phenotypic evaluation of CT-9 and CT-71 was described in Patent No: WO2005/121364.

CT-9 or CT-71 ligated to binary constructs, comprising the 35S promoter were transformed into tomato plants via Agrobacterium tumefaciens transformation.

60 μL of Agrobacterium tumefaciens LB4404 competent cells (about 10⁹ cells/mL) were transformed with 20 ng of binary plasmid via electroporation, using a MicroPulser electroporator (Biorad), 0.2 cm cuvettes (Biorad) and EC-2 electroporation program (Biorad).

Agrobacterium cells were grown on 0.8 mL LB liquid medium at 28° C. for 3 hrs and 0.2 mL of the cell suspension were plated on LB-agar plates supplemented with the antibiotics streptomycin 300 mg/L (for Agrobacterium strain LB4404) and kanamycin 50 mg/L (Sigma). Plates were then incubated at 28° C. for 48 hrs. Agrobacterium colonies were grown and PCR amplification was performed on Agrobacterium cells, using primers which were designed to span the inserted sequence in the binary vector.

PCR products were separated on 1.5% agarose gels and product sizes were determined by comparing to DNA ladder (MBI Fermentas). PCR products with the predicted size were sequenced using the primers which were used for the PCR amplification. Sequencing of the inserted sequence was performed to verify that the right clones were introduced into the Agrobacterium cells. DNA sequencing was effected using ABI 377 sequencer (Amersham Biosciences Inc.).

Transformation of Micro-Tom Tomato Plants with CT_(—)9 or CT-71—

Tomato (Lycopersicon esculentum, var MicroTom) transformation and cultivation of transgenic plants was effected according to Curtis et al. 1995 Methods Mol Biol. 1995; 44:59-70., and Meissner et. al. 2000. Plant J. 2000 May; 22(3):265-74. Following transformation, T1 MicroTom tomato plants were grown in a mix contained in 1000 ml pots, until fruit set and T2 seeds harvesting. Transgenic micro-tom tomato plants over expressing the CT-9 or CT-71 genes under the regulation of the 35S promoter were cross-pollinated with M82 commercial variety plants. Taking randomly four plants originated from four different insertion events representing the position effect. The F1 hybrids which include the transgene were used for further evaluation. As a negative control, non-transgenic plants that segregated from the same transgenic populations were used. To distinguish between transgenic and non transgenic plants a PCR screening was effected using primers of the NPTII gene as described in example 6.

Results

At the fruit ripening stage of about 90% red fruits, plants were evaluated and fruits were harvested. Plant performance was evaluated by measuring mass of the canopies, root length and mass. The yield was measured by taking green and red full size fruits for each plant. The results were analyzed using one side Anova test and summarized in Table 48, below.

TABLE 48 Total fruit yield of the plant lines grown under severe water stress (WLI-2) expressing CT-9 gene compared to control plants. Mean of total full size Mean of total full size Name of fruit weight per plant (g) - fruit weight per plant (g) - the line gene construct best performing event Control - 656 c 656 c non transgenic plants CT-71 692 bc 707 bc CT-9 782 a 840 a a, b, c—Levels not connected by same letter are statistically significantly different at P < 0.05

The transgenic lines overexpressing CT-9 showed significantly higher fruit yield under severe water deficiency conditions (WLI-2) compared to control plants.

The improvement in yield was observed also under regular water irrigation both for lines expressing CT-9 and CT-71 (see Table 49, below).

TABLE 49 Total fruit yield of the lines over expressing CT-9 compared to control plants grown under favorable water irrigation (WLI-0) Mean of total full size Mean of total full size Name of fruit weight per plant (g) - fruit weight per plant (g) - the line gene construct best performing event Negative  820 b  820 b control - non transgenic plants CT-71 1010 a 1046 a CT-9  993 a  997 ab a, b, c—Levels not connected by same letter are statistically significantly different at P < 0.05

Example 11 Plants Overexpressing FUE_(—)34_Evo are Characterized by Enhanced Lateral Branching

Control of lateral buds activation can have an important role in modern agriculture and breeding of flowers and ornaments. In the case of modern maize breeding, breeders worked for many years towards the reduction of tillers (lateral branches) in order to create single husk plants that reach maturation concurrently. On the other hand, control of tillering in rice breeding has also importance since multiple tillers will allow the production of several panicles on the same plant while overtillering has deleterious effects on the plant. Similarly, lateral branching is important for ornamentals, for example to produce multiple flowers from the same stem, or to produce single large flowers from each stem.

As shown in FIG. 8 plants expressing exogenous FUE_(—)34_Evo are characterized by multiple branching of the shoot. Expression of FUE_(—)34 Evo (SED ID No: 54) under a constitutive ubiquitous promoter caused unusually active lateral branching phenotype. All the transgenic events obtained with these constructs display this particular branching phenotype at every node. This phenotype can be a result of the loss of the plant apical dominance or more likely to the continuous expression of Evo_(—)34_Evo under an ubiquitous constitutive promoter. Evo_(—)34 is a MADS box transcription factor that contains in addition putative phosphorylation sites for cAMP- and cGMP-dependent protein kinase, Casein kinase II and Protein kinase C. Expression under a root preferred promoter such as RootP caused the creation of a compact highly branched root phenotype. FUE_(—)34_Evo can be therefore used for example to engineer plants with controlled branching adding a constitutive or inducible promoter active at certain anatomical parts of the plant and/or at certain developing stages. Similarly the gene can be silenced and in this way tillering or lateral branching will be highly likely avoided. Another potential use for this gene is for MAS (Marker assisted breeding).

Example 12 Homologous and Orthologous Sequences

Table 50 lists a summary of orthologous and homologous sequences of the polynucleotide sequences and polypeptide sequences of the invention identified using BLAST (TBLASTX program) having at least 85% similarity on at least 85% of the entire protein length.

TABLE 50 SEQ ID NO: Gene Polynucleotide/polypeptide organism Species coverage percent_identity FUE_1 219/768  maize Zea mays 100 100 FUE_1 220/769  rice Oryza sativa 89.47 77.44 FUE_1 221/770  sorghum Sorghum bicolor 87.22 81.95 FUE_1 222/771  sugarcane Saccharum officinarum 88.72 84.96 FUE_1 223/772  wheat Triticum spp. 96.99 96.24 FUE_1 224/773  wheat Triticum spp. 100 98.5 FUE_2 225/774  maize Zea mays 98.48 95.45 FUE_2 226/775  maize Zea mays 100 100 FUE_2 227/776  maize Zea mays 100 100 FUE_2 228/777  sorghum Sorghum bicolor 89.39 84.85 FUE_2 229/778  sorghum Sorghum bicolor 89.39 84.85 FUE_2 230/779  sorghum Sorghum bicolor 89.39 84.85 FUE_2 231/780  wheat Triticum spp. 100 100 FUE_3 232/781  maize Zea mays 92.08 88.12 FUE_3 233/782  maize Zea mays 100 99.01 FUE_3 234/783  maize Zea mays 100 100 FUE_3 235/784  maize Zea mays 100 100 FUE_3 236/785  sorghum Sorghum bicolor 88.12 85.15 FUE_3 237/786  sorghum Sorghum bicolor 88.12 85.15 FUE_3 238/787  sugarcane Saccharum officinarum 96.04 91.09 FUE_3 239/788  wheat Triticum spp. 100 99.01 FUE_4 240/789  maize Zea mays 97.63 96.45 FUE_5 241/790  barley Hordeum vulgare 89.68 76.98 FUE_5 242/791  barley Hordeum vulgare 89.68 76.98 FUE_5 243/792  cotton Gossypiumssp. 85.71 72.22 FUE_5 244/793  cotton Gossypiumssp. 85.71 72.22 FUE_5 245/794  maize Zea mays 91.27 77.78 FUE_5 246/795  maize Zea mays 88.89 80.16 FUE_5 247/796  maize Zea mays 88.89 80.16 FUE_5 248/797  maize Zea mays 98.41 95.24 FUE_5 249/798  maize Zea mays 99.21 99.21 FUE_5 250/799  maize Zea mays 100 100 FUE_5 251/800  rice Oryza sativa 86.51 80.16 FUE_5 252/801  rice Oryza sativa 86.51 80.16 FUE_5 253/802  rice Oryza sativa 91.27 83.33 FUE_5 254/803  rice Oryza sativa 92.06 83.33 FUE_5 255/804  sesame Sesamum indicum 85.71 73.81 FUE_5 256/805  sesame Sesamum indicum 85.71 74.6 FUE_5 257/806  sorghum Sorghum bicolor 88.1 78.57 FUE_5 258/807  sorghum Sorghum bicolor 97.62 92.06 FUE_5 259/808  sorghum Sorghum bicolor 97.62 92.06 FUE_5 260/809  sugarcane Saccharum officinarum 88.89 80.95 FUE_5 261/810  sugarcane Saccharum officinarum 97.62 93.65 FUE_5 262/811  tobacco Nicotiana spp. 85.71 70.63 FUE_5 263/812  tobacco Nicotiana spp. 85.71 70.63 FUE_5 264/813  tobacco Nicotiana spp. 85.71 70.63 FUE_5 265/814  wheat Triticum spp. 90.48 76.98 FUE_5 266/815  wheat Triticum spp. 91.27 76.98 FUE_5 267/816  wheat Triticum spp. 90.48 76.98 FUE_5 268/817  wheat Triticum spp. 91.27 77.78 FUE_5 269/818  wheat Triticum spp. 85.71 79.37 FUE_40 270/819  barley Hordeum vulgare 85.89 77.91 FUE_40 271/820  maize Zea mays 85.89 80.37 FUE_40 272/821  maize Zea mays 85.89 80.37 FUE_40 273/822  maize Zea mays 100 100 FUE_40 274/823  rice Oryza sativa 85.89 71.17 FUE_40 275/824  sorghum Sorghum bicolor 86.5 73.01 FUE_40 276/825  sorghum Sorghum bicolor 86.5 73.01 FUE_40 277/826  sorghum Sorghum bicolor 90.8 86.5 FUE_40 278/827  sorghum Sorghum bicolor 91.41 87.73 FUE_40 279/828  sorghum Sorghum bicolor 91.41 87.73 FUE_7 280/829  maize Zea mays 98.63 98.63 FUE_7 281/830  sorghum Sorghum bicolor 87.67 86.3 FUE_9 282/831  maize Zea mays 100 100 FUE_9 283/832  sorghum Sorghum bicolor 94.35 90.4 FUE_10 284/833  maize Zea mays 99.14 99.14 FUE_11 285/834  maize Zea mays 96.83 94.44 FUE_11 286/835  maize Zea mays 95.24 94.44 FUE_11 287/836  maize Zea mays 97.62 96.03 FUE_11 288/837  maize Zea mays 97.62 96.03 FUE_11 289/838  maize Zea mays 97.62 96.03 FUE_11 290/839  maize Zea mays 98.41 96.83 FUE_11 291/840  maize Zea mays 96.83 96.83 FUE_11 292/841  maize Zea mays 97.62 97.62 FUE_11 293/842  maize Zea mays 99.21 99.21 FUE_11 294/843  sorghum Sorghum bicolor 91.27 85.71 FUE_11 295/844  sorghum Sorghum bicolor 91.27 85.71 FUE_11 296/845  sugarcane Saccharum officinarum 88.1 84.13 FUE_11 297/846  wheat Triticum spp. 96.03 95.24 FUE_12 298/847  maize Zea mays 99.2 98.93 FUE_12 299/848  maize Zea mays 99.47 99.2 FUE_12 300/849  maize Zea mays 99.73 99.2 FUE_12 301/850  rice Oryza sativa 90.67 80.53 FUE_13 302/851  maize Zea mays 100 100 FUE_14 303/852  barley Hordeum vulgare 85.33 77.33 FUE_14 304/853  barley Hordeum vulgare 85.78 79.56 FUE_14 305/854  barley Hordeum vulgare 87.11 80.44 FUE_14 306/855  barley Hordeum vulgare 88.44 81.78 FUE_14 307/856  barley Hordeum vulgare 88.44 81.78 FUE_14 308/857  maize Zea mays 85.78 75.11 FUE_14 309/858  maize Zea mays 85.78 75.11 FUE_14 310/859  maize Zea mays 86.22 76 FUE_14 311/860  maize Zea mays 86.22 76 FUE_14 312/861  maize Zea mays 87.11 78.22 FUE_14 313/862  maize Zea mays 85.33 81.33 FUE_14 314/863  maize Zea mays 92.44 88.44 FUE_14 315/864  maize Zea mays 92.44 88.89 FUE_14 316/865  maize Zea mays 92.89 88.89 FUE_14 317/866  maize Zea mays 92.89 89.33 FUE_14 318/867  maize Zea mays 93.33 89.33 FUE_14 319/868  maize Zea mays 93.33 89.33 FUE_14 320/869  maize Zea mays 94.67 90.22 FUE_14 321/870  maize Zea mays 100 100 FUE_14 322/871  maize Zea mays 100 100 FUE_14 323/872  rice Oryza sativa 85.33 73.33 FUE_14 324/873  rice Oryza sativa 85.33 73.33 FUE_14 325/874  rice Oryza sativa 85.33 74.22 FUE_14 326/875  rice Oryza sativa 85.33 74.22 FUE_14 327/876  rice Oryza sativa 88 77.78 FUE_14 328/877  rice Oryza sativa 88 77.78 FUE_14 329/878  rice Oryza sativa 85.78 79.56 FUE_14 330/879  rice Oryza sativa 85.78 79.56 FUE_14 331/880  rice Oryza sativa 86.67 80.89 FUE_14 332/881  rice Oryza sativa 86.67 81.33 FUE_14 333/882  rice Oryza sativa 86.67 81.33 FUE_14 334/883  rice Oryza sativa 88 81.78 FUE_14 335/884  rice Oryza sativa 87.56 81.78 FUE_14 336/885  rice Oryza sativa 88 81.78 FUE_14 337/886  rice Oryza sativa 87.56 81.78 FUE_14 338/887  rice Oryza sativa 87.56 82.22 FUE_14 339/888  rice Oryza sativa 87.56 82.22 FUE_14 340/889  rice Oryza sativa 87.56 82.67 FUE_14 341/890  rice Oryza sativa 87.56 82.67 FUE_14 342/891  rice Oryza sativa 88 83.11 FUE_14 343/892  rice Oryza sativa 88 83.11 FUE_14 344/893  sorghum Sorghum bicolor 86.22 76.44 FUE_14 345/894  sorghum Sorghum bicolor 86.22 76.44 FUE_14 346/895  sorghum Sorghum bicolor 86.22 77.33 FUE_14 347/896  sorghum Sorghum bicolor 86.67 77.78 FUE_14 348/897  sorghum Sorghum bicolor 93.33 89.78 FUE_14 349/898  sorghum Sorghum bicolor 93.78 89.78 FUE_14 350/899  sorghum Sorghum bicolor 93.78 89.78 FUE_14 351/900  sorghum Sorghum bicolor 93.78 90.22 FUE_14 352/901  sorghum Sorghum bicolor 93.78 90.22 FUE_14 353/902  sorghum Sorghum bicolor 94.67 90.67 FUE_14 354/903  wheat Triticum spp. 87.11 80.44 FUE_14 355/904  wheat Triticum spp. 88.89 80.89 FUE_14 356/905  wheat Triticum spp. 87.56 81.33 FUE_14 357/906  wheat Triticum spp. 87.11 81.33 FUE_14 358/907  wheat Triticum spp. 88 81.78 FUE_14 359/908  wheat Triticum spp. 89.33 81.78 FUE_14 360/909  wheat Triticum spp. 90.22 83.11 FUE_14 361/910  wheat Triticum spp. 89.33 83.11 FUE_15 362/911  maize Zea mays 100 100 FUE_15 363/912  sorghum Sorghum bicolor 89.32 88.26 FUE_16 364/913  maize Zea mays 88.21 83.59 FUE_16 365/914  maize Zea mays 100 100 FUE_16 366/915  sorghum Sorghum bicolor 87.69 83.59 FUE_17 367/916  barley Hordeum vulgare 88.84 79.68 FUE_17 368/917  barley Hordeum vulgare 88.84 79.68 FUE_17 369/918  maize Zea mays 94.42 88.45 FUE_17 370/919  maize Zea mays 100 100 FUE_17 371/920  maize Zea mays 100 100 FUE_17 372/921  rice Oryza sativa 89.24 78.49 FUE_17 373/922  sorghum Sorghum bicolor 96.02 92.03 FUE_17 374/923  wheat Triticum spp. 88.45 79.28 FUE_17 375/924  wheat Triticum spp. 89.64 80.08 FUE_30 376/925  maize Zea mays 97.8 97.8 FUE_30 377/926  maize Zea mays 98.31 97.97 FUE_30 378/927  maize Zea mays 99.66 99.66 FUE_30 379/928  maize Zea mays 99.83 99.83 FUE_30 380/929  maize Zea mays 99.83 99.83 FUE_30 381/930  rice Oryza sativa 87.46 79.15 FUE_30 382/931  rice Oryza sativa 87.46 79.15 FUE_30 383/932  sorghum Sorghum bicolor 91.69 85.93 FUE_30 384/933  sugarcane Saccharum officinarum 92.03 87.29 FUE_31 385/934  maize Zea mays 99.15 98.98 FUE_31 386/935  rice Oryza sativa 88.05 81.74 FUE_31 387/936  rice Oryza sativa 88.05 81.74 FUE_31 388/937  wheat Triticum spp. 85.15 75.94 FUE_32 389/938  maize Zea mays 100 100 FUE_32 390/939  rice Oryza sativa 89.47 85.65 FUE_33 391/940  barley Hordeum vulgare 92.8 88.64 FUE_33 392/941  barley Hordeum vulgare 93.63 89.75 FUE_33 393/942  maize Zea mays 99.72 99.72 FUE_33 394/943  maize Zea mays 99.72 99.72 FUE_33 395/944  rice Oryza sativa 93.35 90.3 FUE_33 396/945  rice Oryza sativa 93.63 90.58 FUE_33 397/946  sorghum Sorghum bicolor 85.32 75.35 FUE_33 398/947  sorghum Sorghum bicolor 85.32 75.35 FUE_33 399/948  sorghum Sorghum bicolor 97.51 96.68 FUE_33 400/949  sorghum Sorghum bicolor 97.78 96.95 FUE_33 401/950  sugarcane Saccharum officinarum 85.04 75.9 FUE_33 402/951  sugarcane Saccharum officinarum 97.51 96.68 FUE_33 403/952  wheat Triticum spp. 93.35 89.75 FUE_34_Evo 404/953  maize Zea mays 96.25 94.58 FUE_34_Evo 405/954  maize Zea mays 96.25 94.58 FUE_34_Evo 406/955  rice Oryza sativa 86.25 76.67 FUE_34_Evo 407/956  rice Oryza sativa 87.92 78.33 FUE_34_Evo 408/957  rice Oryza sativa 92.5 85.83 FUE_34_Evo 409/958  rice Oryza sativa 92.92 86.25 FUE_34_Evo 410/959  wheat Triticum spp. 87.5 78.75 FUE_34_Pat 411/960  maize Zea mays 100 100 FUE_34_Pat 412/961  rice Oryza sativa 85.83 76.67 FUE_34_Pat 413/962  rice Oryza sativa 87.5 78.33 FUE_34_Pat 414/963  rice Oryza sativa 92.08 85.42 FUE_34_Pat 415/964  rice Oryza sativa 92.5 85.83 FUE_34_Pat 416/965  wheat Triticum spp. 87.5 78.75 FUE_35 417/966  maize Zea mays 98.41 96.03 FUE_35 418/967  maize Zea mays 100 97.62 FUE_35 419/968  maize Zea mays 100 100 FUE_36 420/969  Arabidopsis Arabidopsis thaliana 87.43 74.86 FUE_36 421/970  Arabidopsis Arabidopsis thaliana 87.98 75.41 FUE_36 422/971  Arabidopsis Arabidopsis thaliana 90.16 77.87 FUE_36 423/972  Arabidopsis Arabidopsis thaliana 90.16 77.87 FUE_36 424/973  Arabidopsis Arabidopsis thaliana 90.98 80.87 FUE_36 425/974  Arabidopsis Arabidopsis thaliana 92.35 82.51 FUE_36 426/975  Arabidopsis Arabidopsis thaliana 92.35 82.51 FUE_36 427/976  barley Hordeum vulgare 87.43 79.51 FUE_36 428/977  barley Hordeum vulgare 87.43 79.51 FUE_36 429/978  barley Hordeum vulgare 87.7 80.05 FUE_36 430/979  barley Hordeum vulgare 92.35 86.34 FUE_36 431/980  barley Hordeum vulgare 97.27 93.72 FUE_36 432/981  barley Hordeum vulgare 97.27 93.72 FUE_36 433/982  cotton Gossypium ssp. 87.16 77.87 FUE_36 434/983  cotton Gossypium ssp. 85.79 78.42 FUE_36 435/984  cotton Gossypium ssp. 89.89 82.24 FUE_36 436/985  cotton Gossypium ssp. 90.16 82.79 FUE_36 437/986  maize Zea mays 91.8 84.97 FUE_36 438/987  maize Zea mays 98.91 98.91 FUE_36 439/988  maize Zea mays 98.91 98.91 FUE_36 440/989  maize Zea mays 100 99.73 FUE_36 441/990  poplar Populus spp 91.53 83.06 FUE_36 442/991  poplar Populus spp 91.53 83.33 FUE_36 443/992  rice Oryza sativa 90.98 83.06 FUE_36 444/993  rice Oryza sativa 90.98 83.06 FUE_36 445/994  rice Oryza sativa 91.26 86.61 FUE_36 446/995  rice Oryza sativa 91.26 86.61 FUE_36 447/996  rice Oryza sativa 96.17 92.9 FUE_36 448/997  rice Oryza sativa 96.17 92.9 FUE_36 449/998  sorghum Sorghum bicolor 92.62 87.16 FUE_36 450/999  sorghum Sorghum bicolor 99.18 99.18 FUE_36 451/1000 sorghum Sorghum bicolor 99.18 99.18 FUE_36 452/1001 soybean Glycine max 87.7 77.87 FUE_36 453/1002 soybean Glycine max 89.34 78.96 FUE_36 454/1003 soybean Glycine max 89.34 79.51 FUE_36 455/1004 soybean Glycine max 89.34 79.51 FUE_36 456/1005 soybean Glycine max 89.62 79.78 FUE_36 457/1006 soybean Glycine max 92.35 84.15 FUE_36 458/1007 sugarcane Saccharum officinarum 98.91 98.63 FUE_36 459/1008 sugarcane Saccharum officinarum 98.91 98.91 FUE_36 460/1009 sunflower Helianthus annuus 87.43 76.78 FUE_36 461/1010 tobacco Nicotiana spp. 91.53 83.61 FUE_36 462/1011 tomato Solanum lycopersicum 87.7 78.69 FUE_36 463/1012 tomato Solanum lycopersicum 87.7 78.69 FUE_36 464/1013 tomato Solanum lycopersicum 92.62 84.7 FUE_36 465/1014 wheat Triticum spp. 86.89 80.05 FUE_36 466/1015 wheat Triticum spp. 91.53 85.52 FUE_36 467/1016 wheat Triticum spp. 97.27 93.99 FUE_37 468/1017 barley Hordeum vulgare 91.55 83.1 FUE_37 469/1018 barley Hordeum vulgare 91.55 83.1 FUE_37 470/1019 maize Zea mays 100 100 FUE_37 471/1020 rice Oryza sativa 95.07 88.03 FUE_37 472/1021 rice Oryza sativa 95.07 88.03 FUE_37 473/1022 sugarcane Saccharum officinarum 97.18 93.66 FUE_37 474/1023 wheat Triticum spp. 91.55 83.1 FUE_38 475/1024 Arabidopsis Arabidopsis thaliana 86.79 69.97 FUE_38 476/1025 Arabidopsis Arabidopsis thaliana 86.79 69.97 FUE_38 477/1026 Arabidopsis Arabidopsis thaliana 86.79 70.27 FUE_38 478/1027 Arabidopsis Arabidopsis thaliana 85.89 73.27 FUE_38 479/1028 Arabidopsis Arabidopsis thaliana 85.89 73.27 FUE_38 480/1029 Arabidopsis Arabidopsis thaliana 85.89 73.27 FUE_38 481/1030 barley Hordeum vulgare 85.29 67.57 FUE_38 482/1031 barley Hordeum vulgare 85.29 67.57 FUE_38 483/1032 barley Hordeum vulgare 85.59 68.17 FUE_38 484/1033 barley Hordeum vulgare 85.89 69.37 FUE_38 485/1034 barley Hordeum vulgare 85.89 69.37 FUE_38 486/1035 barley Hordeum vulgare 86.19 71.17 FUE_38 487/1036 barley Hordeum vulgare 86.19 71.17 FUE_38 488/1037 barley Hordeum vulgare 85.59 73.87 FUE_38 489/1038 cotton Gossypium ssp. 85.89 69.97 FUE_38 490/1039 cotton Gossypium ssp. 85.29 69.97 FUE_38 491/1040 cotton Gossypium ssp. 85.89 72.97 FUE_38 492/1041 cotton Gossypium ssp. 87.09 72.97 FUE_38 493/1042 cotton Gossypium ssp. 85.89 73.27 FUE_38 494/1043 cotton Gossypium ssp. 86.79 73.87 FUE_38 495/1044 cotton Gossypium ssp. 86.49 74.17 FUE_38 496/1045 cotton Gossypium ssp. 89.79 77.48 FUE_38 497/1046 grape Vitis ssp. 86.79 72.97 FUE_38 498/1047 grape Vitis ssp. 86.79 72.97 FUE_38 499/1048 grape Vitis ssp. 90.09 80.18 FUE_38 500/1049 maize Zea mays 85.29 67.87 FUE_38 501/1050 maize Zea mays 85.29 67.87 FUE_38 502/1051 maize Zea mays 85.29 68.47 FUE_38 503/1052 maize Zea mays 85.59 71.17 FUE_38 504/1053 maize Zea mays 85.89 71.17 FUE_38 505/1054 maize Zea mays 85.89 71.17 FUE_38 506/1055 maize Zea mays 85.89 71.17 FUE_38 507/1056 maize Zea mays 85.89 71.47 FUE_38 508/1057 maize Zea mays 85.89 71.47 FUE_38 509/1058 maize Zea mays 86.19 73.87 FUE_38 510/1059 maize Zea mays 86.19 74.77 FUE_38 511/1060 maize Zea mays 86.19 74.77 FUE_38 512/1061 maize Zea mays 100 100 FUE_38 513/1062 poplar Populus spp 89.49 79.28 FUE_38 514/1063 poplar Populus spp 89.49 79.88 FUE_38 515/1064 rice Oryza sativa 85.59 68.17 FUE_38 516/1065 rice Oryza sativa 85.59 68.17 FUE_38 517/1066 rice Oryza sativa 85.59 68.77 FUE_38 518/1067 rice Oryza sativa 85.59 68.77 FUE_38 519/1068 rice Oryza sativa 87.39 72.07 FUE_38 520/1069 rice Oryza sativa 87.39 72.07 FUE_38 521/1070 rice Oryza sativa 86.79 73.57 FUE_38 522/1071 rice Oryza sativa 86.79 73.57 FUE_38 523/1072 rice Oryza sativa 85.89 73.87 FUE_38 524/1073 rice Oryza sativa 85.89 73.87 FUE_38 525/1074 rice Oryza sativa 86.79 75.38 FUE_38 526/1075 rice Oryza sativa 86.79 75.38 FUE_38 527/1076 rice Oryza sativa 96.4 91.59 FUE_38 528/1077 rice Oryza sativa 96.4 91.59 FUE_38 529/1078 sorghum Sorghum bicolor 85.29 67.87 FUE_38 530/1079 sorghum Sorghum bicolor 85.29 67.87 FUE_38 531/1080 sorghum Sorghum bicolor 86.19 69.07 FUE_38 532/1081 sorghum Sorghum bicolor 85.89 71.77 FUE_38 533/1082 sorghum Sorghum bicolor 87.39 72.07 FUE_38 534/1083 sorghum Sorghum bicolor 99.1 97.6 FUE_38 535/1084 sorghum Sorghum bicolor 99.1 97.6 FUE_38 536/1085 soybean Glycine max 85.29 67.27 FUE_38 537/1086 soybean Glycine max 85.29 67.87 FUE_38 538/1087 soybean Glycine max 85.89 69.67 FUE_38 539/1088 soybean Glycine max 86.49 71.47 FUE_38 540/1089 soybean Glycine max 86.79 71.77 FUE_38 541/1090 soybean Glycine max 85.89 72.67 FUE_38 542/1091 soybean Glycine max 85.29 73.27 FUE_38 543/1092 soybean Glycine max 86.79 74.17 FUE_38 544/1093 soybean Glycine max 86.79 74.17 FUE_38 545/1094 soybean Glycine max 85.59 75.38 FUE_38 546/1095 soybean Glycine max 88.29 77.78 FUE_38 547/1096 soybean Glycine max 88.29 78.08 FUE_38 548/1097 soybean Glycine max 88.89 78.38 FUE_38 549/1098 sugarcane Saccharum officinarum 85.29 67.87 FUE_38 550/1099 sugarcane Saccharum officinarum 86.49 72.07 FUE_38 551/1100 sugarcane Saccharum officinarum 86.79 75.08 FUE_38 552/1101 sugarcane Saccharum officinarum 99.4 97.9 FUE_38 553/1102 tobacco Nicotiana spp. 86.79 72.97 FUE_38 554/1103 tobacco Nicotiana spp. 86.79 72.97 FUE_38 555/1104 tobacco Nicotiana spp. 87.39 75.38 FUE_38 556/1105 tobacco Nicotiana spp. 87.99 76.28 FUE_38 557/1106 tobacco Nicotiana spp. 87.99 76.28 FUE_38 558/1107 tomato Solanum lycopersicum 86.19 69.67 FUE_38 559/1108 tomato Solanum lycopersicum 86.49 72.37 FUE_38 560/1109 tomato Solanum lycopersicum 90.69 78.38 FUE_38 561/1110 tomato Solanum lycopersicum 90.69 78.38 FUE_38 562/1111 wheat Triticum spp. 85.59 68.17 FUE_38 563/1112 wheat Triticum spp. 85.89 69.67 FUE_38 564/1113 wheat Triticum spp. 86.19 71.17 FUE_38 565/1114 wheat Triticum spp. 85.89 71.47 FUE_38 566/1115 wheat Triticum spp. 85.89 71.47 FUE_38 567/1116 wheat Triticum spp. 86.49 71.77 FUE_38 568/1117 wheat Triticum spp. 85.59 73.57 FUE_38 569/1118 wheat Triticum spp. 93.69 86.49 FUE_39 570/1119 Arabidopsis Arabidopsis thaliana 91.93 81.17 FUE_39 571/1120 Arabidopsis Arabidopsis thaliana 91.93 81.17 FUE_39 572/1121 Arabidopsis Arabidopsis thaliana 91.93 81.17 FUE_39 573/1122 Arabidopsis Arabidopsis thaliana 91.48 81.61 FUE_39 574/1123 Arabidopsis Arabidopsis thaliana 91.48 81.61 FUE_39 575/1124 canola Brassica ssp. 90.13 79.82 FUE_39 576/1125 barley Hordeum vulgare 93.27 79.82 FUE_39 577/1126 barley Hordeum vulgare 93.27 79.82 FUE_39 578/1127 barley Hordeum vulgare 90.58 80.72 FUE_39 579/1128 barley Hordeum vulgare 90.58 80.72 FUE_39 580/1129 barley Hordeum vulgare 98.65 94.62 FUE_39 581/1130 barley Hordeum vulgare 98.65 94.62 FUE_39 582/1131 cotton Gossypium ssp. 93.27 80.72 FUE_39 583/1132 cotton Gossypium ssp. 93.27 81.61 FUE_39 584/1133 cotton Gossypium ssp. 94.17 82.06 FUE_39 585/1134 cotton Gossypium ssp. 94.62 82.06 FUE_39 586/1135 cotton Gossypium ssp. 94.17 82.06 FUE_39 587/1136 cotton Gossypium ssp. 94.17 82.96 FUE_39 588/1137 cotton Gossypium ssp. 95.07 83.86 FUE_39 589/1138 grape Vitis ssp. 93.72 82.96 FUE_39 590/1139 grape Vitis ssp. 93.27 82.96 FUE_39 591/1140 grape Vitis ssp. 93.72 82.96 FUE_39 592/1141 maize Zea mays 94.62 78.92 FUE_39 593/1142 maize Zea mays 93.27 79.82 FUE_39 594/1143 maize Zea mays 92.83 80.27 FUE_39 595/1144 maize Zea mays 93.27 80.72 FUE_39 596/1145 maize Zea mays 94.17 80.72 FUE_39 597/1146 maize Zea mays 100 100 FUE_39 598/1147 maize Zea mays 100 100 FUE_39 599/1148 peach Prunus persica 93.27 81.17 FUE_39 600/1149 poplar Populus spp 93.27 82.06 FUE_39 601/1150 poplar Populus spp 93.27 82.06 FUE_39 602/1151 poplar Populus spp 92.38 82.51 FUE_39 603/1152 poplar Populus spp 94.17 82.96 FUE_39 604/1153 poplar Populus spp 94.17 82.96 FUE_39 605/1154 rice Oryza sativa 94.62 80.72 FUE_39 606/1155 rice Oryza sativa 94.62 81.17 FUE_39 607/1156 rice Oryza sativa 93.72 82.96 FUE_39 608/1157 rice Oryza sativa 93.72 82.96 FUE_39 609/1158 rice Oryza sativa 95.07 91.93 FUE_39 610/1159 rice Oryza sativa 95.07 91.93 FUE_39 611/1160 sorghum Sorghum bicolor 95.52 81.17 FUE_39 612/1161 sorghum Sorghum bicolor 95.52 81.17 FUE_39 613/1162 sorghum Sorghum bicolor 99.55 98.65 FUE_39 614/1163 soybean Glycine max 93.72 82.51 FUE_39 615/1164 soybean Glycine max 93.72 82.51 FUE_39 616/1165 soybean Glycine max 94.62 83.41 FUE_39 617/1166 soybean Glycine max 94.62 83.41 FUE_39 618/1167 sugarcane Saccharum officinarum 94.17 81.61 FUE_39 619/1168 sunflower Helianthus annuus 91.03 77.13 FUE_39 620/1169 sunflower Helianthus annuus 93.27 82.96 FUE_39 621/1170 tobacco Nicotiana spp. 87 77.58 FUE_39 622/1171 tobacco Nicotiana spp. 89.69 78.92 FUE_39 623/1172 tobacco Nicotiana spp. 92.83 82.51 FUE_39 624/1173 tomato Solanum lycopersicum 89.69 79.82 FUE_39 625/1174 tomato Solanum lycopersicum 91.48 81.17 FUE_39 626/1175 tomato Solanum lycopersicum 92.38 82.51 FUE_39 627/1176 wheat Triticum spp. 93.27 79.82 FUE_39 628/1177 wheat Triticum spp. 92.83 82.96 FUE_39 629/1178 wheat Triticum spp. 99.1 94.62 FUE_41 630/1179 maize Zea mays 98.76 98.76 FUE_41 631/1180 maize Zea mays 100 100 FUE_41 632/1181 sorghum Sorghum bicolor 96.27 92.55 FUE_41 633/1182 sorghum Sorghum bicolor 96.89 93.79 FUE_41 634/1183 sorghum Sorghum bicolor 96.89 93.79 FUE_43 635/1184 barley Hordeum vulgare 91.27 85.71 FUE_43 636/1185 barley Hordeum vulgare 91.27 85.71 FUE_43 637/1186 maize Zea mays 100 100 FUE_43 638/1187 rice Oryza sativa 90.48 85.71 FUE_43 639/1188 rice Oryza sativa 90.48 85.71 FUE_43 640/1189 sorghum Sorghum bicolor 99.21 97.62 FUE_43 641/1190 sorghum Sorghum bicolor 99.21 97.62 FUE_43 642/1191 sugarcane Saccharum officinarum 86.51 85.71 FUE_43 643/1192 sugarcane Saccharum officinarum 98.41 97.62 FUE_43 644/1193 wheat Triticum spp. 91.27 85.71 FUE_44 645/1194 barley Hordeum vulgare 87.72 83.04 FUE_44 646/1195 barley Hordeum vulgare 88.3 84.21 FUE_44 647/1196 maize Zea mays 98.83 98.25 FUE_44 648/1197 rice Oryza sativa 90.06 80.7 FUE_44 649/1198 rice Oryza sativa 91.81 85.38 FUE_44 650/1199 sorghum Sorghum bicolor 86.55 82.46 FUE_44 651/1200 sorghum Sorghum bicolor 96.49 91.81 FUE_44 652/1201 sugarcane Saccharum officinarum 93.57 86.55 FUE_44 653/1202 sugarcane Saccharum officinarum 94.74 87.72 FUE_44 654/1203 sugarcane Saccharum officinarum 97.08 91.81 FUE_44 655/1204 sugarcane Saccharum officinarum 97.08 92.4 FUE_44 656/1205 wheat Triticum spp. 87.72 83.63 FUE_44 657/1206 wheat Triticum spp. 88.89 84.21 FUE_44 658/1207 wheat Triticum spp. 88.89 84.8 FUE_44 659/1208 wheat Triticum spp. 90.64 85.96 FUE_45 660/1209 barley Hordeum vulgare 86.83 78.44 FUE_45 661/1210 barley Hordeum vulgare 86.83 78.44 FUE_45 662/1211 maize Zea mays 98.2 94.01 FUE_45 663/1212 maize Zea mays 100 100 FUE_45 664/1213 rice Oryza sativa 88.62 80.24 FUE_45 665/1214 rice Oryza sativa 88.62 80.24 FUE_45 666/1215 sorghum Sorghum bicolor 100 98.2 FUE_45 667/1216 sugarcane Saccharum officinarum 100 98.2 FUE_45 668/1217 wheat Triticum spp. 85.03 76.65 FUE_45 669/1218 wheat Triticum spp. 85.03 77.25 FUE_45 670/1219 wheat Triticum spp. 85.03 77.25 FUE_45 671/1220 wheat Triticum spp. 85.63 77.84 FUE_45 672/1221 wheat Triticum spp. 97.01 95.21 FUE_46 673/1222 maize Zea mays 100 100 FUE_47 674/1223 maize Zea mays 89.72 85.77 FUE_47 675/1224 maize Zea mays 100 100 FUE_47 676/1225 maize Zea mays 100 100 FUE_47 677/1226 maize Zea mays 100 100 FUE_47 678/1227 sugarcane Saccharum officinarum 88.14 86.17 FUE_48 679/1228 barley Hordeum vulgare 89.29 81.75 FUE_48 680/1229 maize Zea mays 86.24 79.76 FUE_48 681/1230 maize Zea mays 99.21 99.07 FUE_48 682/1231 maize Zea mays 99.34 99.21 FUE_48 683/1232 rice Oryza sativa 86.64 79.23 FUE_48 684/1233 rice Oryza sativa 86.64 79.23 FUE_48 685/1234 rice Oryza sativa 86.64 79.23 FUE_48 686/1235 rice Oryza sativa 90.34 84.26 FUE_48 687/1236 rice Oryza sativa 90.34 84.26 FUE_48 688/1237 sorghum Sorghum bicolor 94.05 90.61 FUE_48 689/1238 sorghum Sorghum bicolor 94.05 90.61 FUE_48 690/1239 wheat Triticum spp. 89.68 81.35 FUE_48 691/1240 wheat Triticum spp. 89.42 81.61 FUE_49 692/1241 maize Zea mays 96.03 92.82 FUE_49 693/1242 maize Zea mays 98.11 97.35 FUE_49 694/1243 maize Zea mays 99.24 98.68 FUE_49 695/1244 rice Oryza sativa 89.04 81.1 FUE_49 696/1245 rice Oryza sativa 89.04 81.1 FUE_49 697/1246 wheat Triticum spp. 86.96 77.13 FUE_49 698/1247 wheat Triticum spp. 87.33 77.32 FUE_50 699/1248 maize Zea mays 99.73 99.73 FUE_50 700/1249 sugarcane Saccharum officinarum 91.42 88.2 FUE_50 701/1250 sugarcane Saccharum officinarum 92.49 89.28 FUE_51 702/1251 barley Hordeum vulgare 91.5 84.75 FUE_51 703/1252 barley Hordeum vulgare 91.5 84.75 FUE_51 704/1253 barley Hordeum vulgare 94.12 88.45 FUE_51 705/1254 maize Zea mays 100 100 FUE_51 706/1255 rice Oryza sativa 92.59 85.4 FUE_51 707/1256 rice Oryza sativa 92.59 85.4 FUE_51 708/1257 rice Oryza sativa 95.86 93.46 FUE_51 709/1258 rice Oryza sativa 96.08 93.68 FUE_51 710/1259 sorghum Sorghum bicolor 92.16 83.22 FUE_51 711/1260 sorghum Sorghum bicolor 92.16 83.22 FUE_51 712/1261 sugarcane Saccharum officinarum 92.16 83.88 FUE_51 713/1262 sugarcane Saccharum officinarum 98.91 98.26 FUE_51 714/1263 wheat Triticum spp. 91.29 84.97 FUE_51 715/1264 wheat Triticum spp. 94.77 88.89 FUE_52 716/1265 barley Hordeum vulgare 89.35 83.8 FUE_52 717/1266 barley Hordeum vulgare 89.35 83.8 FUE_52 718/1267 maize Zea mays 100 99.77 FUE_52 719/1268 maize Zea mays 100 99.77 FUE_52 720/1269 rice Oryza sativa 90.05 85.88 FUE_52 721/1270 rice Oryza sativa 90.05 86.11 FUE_52 722/1271 rice Oryza sativa 90.05 86.11 FUE_52 723/1272 sorghum Sorghum bicolor 93.06 90.97 FUE_52 724/1273 sugarcane Saccharum officinarum 94.68 92.82 FUE_52 725/1274 wheat Triticum spp. 89.35 83.33 FUE_53 726/1275 barley Hordeum vulgare 86.86 73.73 FUE_53 727/1276 maize Zea mays 95.98 94.37 FUE_53 728/1277 maize Zea mays 100 100 FUE_53 729/1278 rice Oryza sativa 93.57 86.86 FUE_53 730/1279 rice Oryza sativa 93.57 86.86 FUE_53 731/1280 wheat Triticum spp. 89.54 80.43 FUE_54 732/1281 maize Zea mays 90.94 88.77 FUE_54 733/1282 maize Zea mays 96.74 96.74 FUE_54 734/1283 sorghum Sorghum bicolor 87.32 83.7 FUE_54 735/1284 sorghum Sorghum bicolor 87.32 83.7 FUE_54 736/1285 sorghum Sorghum bicolor 90.22 86.59 FUE_54 737/1286 sugarcane Saccharum officinarum 90.94 87.32 FUE_54 738/1287 sugarcane Saccharum officinarum 90.94 87.32 FUE_55 739/1288 maize Zea mays 92.31 89.62 FUE_100 740/1289 barley Hordeum vulgare 88.89 81.77 FUE_100 741/1290 barley Hordeum vulgare 88.89 81.77 FUE_100 742/1291 maize Zea mays 85.19 74.64 FUE_100 743/1292 maize Zea mays 85.19 74.64 FUE_100 744/1293 maize Zea mays 98.29 98.01 FUE_100 745/1294 maize Zea mays 99.72 99.72 FUE_100 746/1295 rice Oryza sativa 86.61 78.92 FUE_100 747/1296 rice Oryza sativa 86.61 78.92 FUE_100 748/1297 sorghum Sorghum bicolor 85.19 74.93 FUE_100 749/1298 sorghum Sorghum bicolor 87.46 78.06 FUE_100 750/1299 sorghum Sorghum bicolor 87.46 78.06 FUE_100 751/1300 sorghum Sorghum bicolor 92.02 88.03 FUE_100 752/1301 sugarcane Saccharum officinarum 89.17 78.63 FUE_100 753/1302 sugarcane Saccharum officinarum 91.45 87.75 FUE_100 754/1303 wheat Triticum spp. 87.18 79.77 FUE_101 755/1304 maize Zea mays 100 100 FUE_101 756/1305 rice Oryza sativa 91.76 84.82 FUE_101 757/1306 rice Oryza sativa 91.76 84.82 FUE_102 758/1307 maize Zea mays 87.2 83.65 FUE_102 759/1308 maize Zea mays 94.31 93.84 FUE_102 760/1309 maize Zea mays 96.21 96.21 FUE_501 761/1310 Arabidopsis Arabidopsis thaliana 87.13 75.86 FUE_501 762/1311 Arabidopsis Arabidopsis thaliana 87.59 76.55 FUE_501 763/1312 Arabidopsis Arabidopsis thaliana 100 100 FUE_502 764/1313 Arabidopsis Arabidopsis thaliana 100 100 FUE_503 765/1314 Arabidopsis Arabidopsis thaliana 100 100 FUE_504 766/1315 Arabidopsis Arabidopsis thaliana 100 100 FUE_505 767/1316 Arabidopsis Arabidopsis thaliana 100 100

It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable subcombination.

Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims. All publications, patents and patent applications and GenBank Accession numbers mentioned in this specification are herein incorporated in their entirety by reference into the specification, to the same extent as if each individual publication, patent or patent application or GenBank Accession number was specifically and individually indicated to be incorporated herein by reference. In addition, citation or identification of any reference in this application shall not be construed as an admission that such reference is available as prior art to the present invention. 

What is claimed is:
 1. A method of increasing abiotic stress tolerance, yield, biomass, growth rate, vigor, nutritional value and/or nitrogen use efficiency of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide which exhibits at least 80% sequence identity to SEQ ID NO: 110-218, 768-1316, 1341 or 1343, thereby increasing the abiotic stress tolerance, yield, biomass, growth rate, vigor, nutritional value and/or nitrogen use efficiency of the plant.
 2. The method of claim 1, wherein said polypeptide exhibits at least 90% sequence identity to the polypeptide selected from the group consisting of SEQ ID NOs: 110-218, 768-1316, 1341 and
 1343. 3. The method of claim 1, wherein said polypeptide exhibits at least 95% sequence identity to the polypeptide selected from the group consisting of SEQ ID NOs: 110-218, 768-1316, 1341 and
 1343. 4. The method of claim 1, wherein said polypeptide is selected from the group consisting of SEQ ID NOs: 110-218, 768-1316, 1341 and
 1343. 5. The method of claim 1, wherein said nucleic acid sequence encoding said polypeptide exhibits at least 80% sequence identity to SEQ ID NO: 1-109, 219-767, 1317-1336, 1340,
 1342. 6. The method of claim 1, wherein said nucleic acid sequence encoding said polypeptide is selected from the group consisting of SEQ ID NOs: 1-109, 219-767, 1317-1336, 1340,
 1342. 7. The method of claim 1, further comprising growing the plant expressing said exogenous polynucleotide under the abiotic stress.
 8. The method of claim 1, wherein said abiotic stress is selected from the group consisting of salinity, drought, water deprivation, flood, freeze, osmoticum, low temperature, high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, nutrient excess, atmospheric pollution and UV irradiation.
 9. The method of claim 1, further comprising selecting the plant expressing said exogenous polynucleotide for an increased abiotic stress tolerance, yield, biomass, growth rate, vigor, nutritional value and/or nitrogen use efficiency as compared to a non-transformed plant which is grown under the same growth conditions.
 10. A method of producing seeds of a crop, comprising: (a) selecting a parent plant being transformed with an exogenous polynucleotide encoding a polypeptide comprising an amino acid sequence which exhibits at least 80% sequence identity to the polypeptide selected from the group consisting of SEQ ID NOs: 110-218, 768-1316, 1341 and 1343, said parent plant exhibits an increased trait selected from the group consisting of: increased abiotic stress tolerance, increased yield, increased biomass, increased growth rate, increased vigor, increased nutritional value and/or increased nitrogen use efficiency as compared to a non-transformed plant which is grown under the same growth conditions, and; (b) growing a seed producing plant from said parent plant resultant of step (a), wherein said seed producing plant which comprises said exogenous polynucleotide has said increased trait, and; (c) producing seeds from said seed producing plant resultant of step (b), thereby producing seeds of the crop.
 11. An isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence which exhibits at least 80% sequence identity to the amino acid sequence set forth in SEQ ID NO: 110-218, 768-1316, 1341 and 1343, wherein said amino acid sequence is capable of increasing abiotic stress tolerance, yield, biomass, growth rate, vigor, nutritional value and/or nitrogen use efficiency of a plant.
 12. The isolated polynucleotide of claim 11, wherein said nucleic acid sequence encoding said polypeptide exhibits at least 80% sequence identity to SEQ ID NO: 1-109, 219-767, 1317-1336, 1340 or
 1342. 13. The isolated polynucleotide of claim 11, wherein said nucleic acid sequence is selected from the group consisting of SEQ ID NOs: 1-109, 219-767, 1317-1336, 1340 and
 1342. 14. A nucleic acid construct comprising the isolated polynucleotide of claim 11, and a promoter for directing transcription of said nucleic acid sequence in a host cell.
 15. A plant cell transformed with the nucleic acid construct of claim
 14. 16. The plant cell of claim 15, wherein said plant cell forms part of a plant.
 17. A transgenic plant comprising the nucleic acid construct of claim
 14. 18. The nucleic acid construct of claim 14, wherein said promoter is a constitutive promoter.
 19. The nucleic acid construct of claim 14, wherein said promoter is a tissue specific promoter or an inducible promoter.
 20. The nucleic acid construct of claim 18, wherein said constitutive promoter is the CaMV promoter set forth by SEQ ID NO: 1337, or the Arabidopsis At6669 promoter set forth by SEQ ID NO:1514.
 21. The nucleic acid construct of claim 19, wherein said tissue specific promoter is the ROOTP promoter set forth by SEQ ID NO:
 1338. 